diff --git a/changelog/unreleased/fix-s3-restore-missing-directory-marker.yml b/changelog/unreleased/fix-s3-restore-missing-directory-marker.yml
new file mode 100644
index 000000000000..fbadc3d512f3
--- /dev/null
+++ b/changelog/unreleased/fix-s3-restore-missing-directory-marker.yml
@@ -0,0 +1,8 @@
+# See https://github.com/apache/solr/blob/main/dev-docs/changelog.adoc
+title: Fix restore failure when S3 backup has no directory marker objects for configset
+type: fixed # added, changed, fixed, deprecated, removed, dependency_update, security, other
+authors:
+  - name: Samuel Verstraete
+links:
+  - name: GitHub PR #4182
+    url: https://github.com/apache/solr/pull/4182
diff --git a/changelog/unreleased/fix-s3-restore-virtual-directory-detection.yml b/changelog/unreleased/fix-s3-restore-virtual-directory-detection.yml
new file mode 100644
index 000000000000..52ba2f614120
--- /dev/null
+++ b/changelog/unreleased/fix-s3-restore-virtual-directory-detection.yml
@@ -0,0 +1,5 @@
+# See https://github.com/apache/solr/blob/main/dev-docs/changelog.adoc
+title: Fix S3 restore failure (NoSuchKey 404) when configset subdirectory markers were removed by aws s3 sync
+type: fixed # added, changed, fixed, deprecated, removed, dependency_update, security, other
+authors:
+  - name: Samuel Verstraete
diff --git a/solr/core/src/java/org/apache/solr/core/backup/BackupManager.java b/solr/core/src/java/org/apache/solr/core/backup/BackupManager.java
index 403dd589b0f9..6504d9f97ad2 100644
--- a/solr/core/src/java/org/apache/solr/core/backup/BackupManager.java
+++ b/solr/core/src/java/org/apache/solr/core/backup/BackupManager.java
@@ -258,7 +258,9 @@ public void uploadConfigDir(
       String sourceConfigName, String targetConfigName, ConfigSetService configSetService)
       throws IOException {
     URI source = repository.resolveDirectory(getZkStateDir(), CONFIG_STATE_DIR, sourceConfigName);
-    if (!repository.exists(source)) {
+    // Use both exists() and listAll() to handle object stores (e.g. S3) where a "directory"
+    // may have no explicit marker object but still contain config files under that prefix.
+    if (!repository.exists(source) && repository.listAll(source).length == 0) {
       throw new IllegalArgumentException("Configset expected at " + source + " does not exist");
     }
     uploadConfigToSolrCloud(configSetService, source, targetConfigName, "");
diff --git a/solr/core/src/test/org/apache/solr/core/backup/BackupManagerUploadConfigTest.java b/solr/core/src/test/org/apache/solr/core/backup/BackupManagerUploadConfigTest.java
new file mode 100644
index 000000000000..a5c948a8aae1
--- /dev/null
+++ b/solr/core/src/test/org/apache/solr/core/backup/BackupManagerUploadConfigTest.java
@@ -0,0 +1,182 @@
+/*
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.apache.solr.core.backup;
+
+import static org.mockito.ArgumentMatchers.any;
+import static org.mockito.ArgumentMatchers.eq;
+import static org.mockito.Mockito.doAnswer;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.verify;
+import static org.mockito.Mockito.when;
+
+import java.net.URI;
+import java.nio.charset.StandardCharsets;
+import org.apache.lucene.store.IOContext;
+import org.apache.lucene.store.IndexInput;
+import org.apache.solr.SolrTestCaseJ4;
+import org.apache.solr.common.cloud.ZkStateReader;
+import org.apache.solr.core.ConfigSetService;
+import org.apache.solr.core.backup.repository.BackupRepository;
+import org.junit.BeforeClass;
+import org.junit.Test;
+
+/**
+ * Unit tests for {@link BackupManager#uploadConfigDir} covering the case where an object-store
+ * backup (e.g. S3) has no explicit directory marker but the config files are still present.
+ */
+public class BackupManagerUploadConfigTest extends SolrTestCaseJ4 {
+
+  @BeforeClass
+  public static void setUpClass() {
+    assumeWorkingMockito();
+  }
+
+  private static final URI BACKUP_PATH = URI.create("s3://bucket/backup/");
+  private static final URI ZK_STATE_URI = URI.create("s3://bucket/backup/zk_backup/");
+  private static final URI CONFIG_DIR_URI =
+      URI.create("s3://bucket/backup/zk_backup/configs/myconfig/");
+  private static final URI SOLRCONFIG_URI =
+      URI.create("s3://bucket/backup/zk_backup/configs/myconfig/solrconfig.xml");
+
+  /**
+   * When the directory marker object is absent (S3 "no-marker" scenario) but config files exist
+   * under the prefix, {@code uploadConfigDir} must succeed and upload those files.
+   *
+   * <p>This is the regression test for the case where a backup was copied through a local
+   * filesystem and re-uploaded to S3, losing the zero-byte directory marker objects in the process.
+   */
+  @Test
+  public void testUploadConfigDir_withoutDirectoryMarker_succeedsWhenFilesPresent()
+      throws Exception {
+    BackupRepository mockRepo = mock(BackupRepository.class);
+    ZkStateReader mockZkStateReader = mock(ZkStateReader.class);
+    ConfigSetService mockConfigSetService = mock(ConfigSetService.class);
+
+    // Simulate S3: no marker object → exists() is false, but listAll() finds the files
+    when(mockRepo.exists(CONFIG_DIR_URI)).thenReturn(false);
+    when(mockRepo.listAll(CONFIG_DIR_URI)).thenReturn(new String[] {"solrconfig.xml"});
+
+    // resolveDirectory chain used by getZkStateDir() and uploadConfigDir()
+    when(mockRepo.resolveDirectory(BACKUP_PATH, BackupManager.ZK_STATE_DIR))
+        .thenReturn(ZK_STATE_URI);
+    when(mockRepo.resolveDirectory(ZK_STATE_URI, BackupManager.CONFIG_STATE_DIR, "myconfig"))
+        .thenReturn(CONFIG_DIR_URI);
+
+    // resolve() used by uploadConfigToSolrCloud() to build the per-file URI
+    when(mockRepo.resolve(CONFIG_DIR_URI, "solrconfig.xml")).thenReturn(SOLRCONFIG_URI);
+    when(mockRepo.getPathType(SOLRCONFIG_URI)).thenReturn(BackupRepository.PathType.FILE);
+
+    // Return minimal valid XML bytes so FileTypeMagicUtil does not reject the file
+    byte[] configBytes = "<config/>".getBytes(StandardCharsets.UTF_8);
+    IndexInput mockInput = mock(IndexInput.class);
+    when(mockInput.length()).thenReturn((long) configBytes.length);
+    doAnswer(
+            invocation -> {
+              byte[] dest = invocation.getArgument(0);
+              int offset = invocation.getArgument(1);
+              System.arraycopy(configBytes, 0, dest, offset, configBytes.length);
+              return null;
+            })
+        .when(mockInput)
+        .readBytes(any(), eq(0), eq(configBytes.length));
+    when(mockRepo.openInput(CONFIG_DIR_URI, "solrconfig.xml", IOContext.DEFAULT))
+        .thenReturn(mockInput);
+
+    BackupManager backupManager = BackupManager.forBackup(mockRepo, mockZkStateReader, BACKUP_PATH);
+
+    // Must not throw even though exists() returned false
+    backupManager.uploadConfigDir("myconfig", "restoredConfig", mockConfigSetService);
+
+    // The config file must have been uploaded to the target configset
+    verify(mockConfigSetService)
+        .uploadFileToConfig(
+            eq("restoredConfig"), eq("solrconfig.xml"), any(byte[].class), eq(false));
+  }
+
+  /**
+   * When neither a directory marker nor any files exist under the config prefix, {@code
+   * uploadConfigDir} must throw {@link IllegalArgumentException}.
+   */
+  @Test
+  public void testUploadConfigDir_throwsWhenTrulyAbsent() throws Exception {
+    BackupRepository mockRepo = mock(BackupRepository.class);
+    ZkStateReader mockZkStateReader = mock(ZkStateReader.class);
+    ConfigSetService mockConfigSetService = mock(ConfigSetService.class);
+
+    URI missingConfigDir = URI.create("s3://bucket/backup/zk_backup/configs/nonexistent/");
+
+    when(mockRepo.exists(missingConfigDir)).thenReturn(false);
+    when(mockRepo.listAll(missingConfigDir)).thenReturn(new String[0]);
+
+    when(mockRepo.resolveDirectory(BACKUP_PATH, BackupManager.ZK_STATE_DIR))
+        .thenReturn(ZK_STATE_URI);
+    when(mockRepo.resolveDirectory(ZK_STATE_URI, BackupManager.CONFIG_STATE_DIR, "nonexistent"))
+        .thenReturn(missingConfigDir);
+
+    BackupManager backupManager = BackupManager.forBackup(mockRepo, mockZkStateReader, BACKUP_PATH);
+
+    assertThrows(
+        IllegalArgumentException.class,
+        () -> backupManager.uploadConfigDir("nonexistent", "target", mockConfigSetService));
+  }
+
+  /**
+   * When the directory marker IS present (the normal case), {@code uploadConfigDir} uses the fast
+   * path via {@code exists()} and must still upload files correctly.
+   */
+  @Test
+  public void testUploadConfigDir_withDirectoryMarker_succeedsNormally() throws Exception {
+    BackupRepository mockRepo = mock(BackupRepository.class);
+    ZkStateReader mockZkStateReader = mock(ZkStateReader.class);
+    ConfigSetService mockConfigSetService = mock(ConfigSetService.class);
+
+    // Marker present → exists() returns true, listAll() should not be called
+    when(mockRepo.exists(CONFIG_DIR_URI)).thenReturn(true);
+    when(mockRepo.listAll(CONFIG_DIR_URI)).thenReturn(new String[] {"solrconfig.xml"});
+
+    when(mockRepo.resolveDirectory(BACKUP_PATH, BackupManager.ZK_STATE_DIR))
+        .thenReturn(ZK_STATE_URI);
+    when(mockRepo.resolveDirectory(ZK_STATE_URI, BackupManager.CONFIG_STATE_DIR, "myconfig"))
+        .thenReturn(CONFIG_DIR_URI);
+
+    when(mockRepo.resolve(CONFIG_DIR_URI, "solrconfig.xml")).thenReturn(SOLRCONFIG_URI);
+    when(mockRepo.getPathType(SOLRCONFIG_URI)).thenReturn(BackupRepository.PathType.FILE);
+
+    byte[] configBytes = "<config/>".getBytes(StandardCharsets.UTF_8);
+    IndexInput mockInput = mock(IndexInput.class);
+    when(mockInput.length()).thenReturn((long) configBytes.length);
+    doAnswer(
+            invocation -> {
+              byte[] dest = invocation.getArgument(0);
+              int offset = invocation.getArgument(1);
+              System.arraycopy(configBytes, 0, dest, offset, configBytes.length);
+              return null;
+            })
+        .when(mockInput)
+        .readBytes(any(), eq(0), eq(configBytes.length));
+    when(mockRepo.openInput(CONFIG_DIR_URI, "solrconfig.xml", IOContext.DEFAULT))
+        .thenReturn(mockInput);
+
+    BackupManager backupManager = BackupManager.forBackup(mockRepo, mockZkStateReader, BACKUP_PATH);
+
+    backupManager.uploadConfigDir("myconfig", "restoredConfig", mockConfigSetService);
+
+    verify(mockConfigSetService)
+        .uploadFileToConfig(
+            eq("restoredConfig"), eq("solrconfig.xml"), any(byte[].class), eq(false));
+  }
+}
diff --git a/solr/modules/s3-repository/src/java/org/apache/solr/s3/S3StorageClient.java b/solr/modules/s3-repository/src/java/org/apache/solr/s3/S3StorageClient.java
index 0add42da2d6b..2f3c2a6329d7 100644
--- a/solr/modules/s3-repository/src/java/org/apache/solr/s3/S3StorageClient.java
+++ b/solr/modules/s3-repository/src/java/org/apache/solr/s3/S3StorageClient.java
@@ -315,6 +315,13 @@ boolean pathExists(String path) throws S3Exception {
   /**
    * Check if path is directory.
    *
+   * <p>A path is considered a directory if either (a) an explicit directory marker object exists
+   * (i.e. a zero-byte object with key {@code path + "/"} and content-type {@code
+   * application/x-directory}), or (b) no such marker exists but at least one object exists whose
+   * key starts with {@code path + "/"} (a "virtual directory"). Case (b) arises after an {@code aws
+   * s3 sync} round-trip, which skips directory marker objects, causing them to be absent in the
+   * target bucket.
+   *
    * @param path to File/Directory in S3.
    * @return true if path is directory, otherwise false.
    */
@@ -329,7 +336,30 @@ boolean isDirectory(String path) throws S3Exception {
       return StrUtils.isNotNullOrEmpty(contentType)
           && contentType.equalsIgnoreCase(S3_DIR_CONTENT_TYPE);
     } catch (NoSuchKeyException nske) {
-      return false;
+      // No explicit directory marker found; fall back to checking whether any objects exist under
+      // this prefix. This handles "virtual directories" that arise after an 'aws s3 sync'
+      // round-trip, which does not preserve directory marker objects (keys ending with '/').
+      return hasChildrenUnderPrefix(s3Path);
+    } catch (SdkException sdke) {
+      throw handleAmazonException(sdke);
+    }
+  }
+
+  /**
+   * Returns {@code true} if at least one object exists in S3 whose key starts with {@code dirPath}.
+   *
+   * <p>Used as a fallback in {@link #isDirectory} when no explicit directory marker object is
+   * present.
+   *
+   * @param dirPath directory path with a trailing {@code /} (as produced by {@link
+   *     #sanitizedDirPath})
+   */
+  private boolean hasChildrenUnderPrefix(String dirPath) throws S3Exception {
+    try {
+      return !s3Client
+          .listObjectsV2(b -> b.bucket(bucketName).prefix(dirPath).maxKeys(1))
+          .contents()
+          .isEmpty();
     } catch (SdkException sdke) {
       throw handleAmazonException(sdke);
     }
diff --git a/solr/modules/s3-repository/src/test/org/apache/solr/s3/S3PathsTest.java b/solr/modules/s3-repository/src/test/org/apache/solr/s3/S3PathsTest.java
index d314855c3b1b..9fd1ecf9a844 100644
--- a/solr/modules/s3-repository/src/test/org/apache/solr/s3/S3PathsTest.java
+++ b/solr/modules/s3-repository/src/test/org/apache/solr/s3/S3PathsTest.java
@@ -163,6 +163,39 @@ public void testDeletePrefix() throws S3Exception {
     assertTrue(client.pathExists("/my-file2"));
   }
 
+  /**
+   * Test that a directory containing objects but lacking an explicit directory marker (i.e. a
+   * "virtual directory") is still recognised as a directory. This mirrors the situation that arises
+   * after an {@code aws s3 sync} round-trip: {@code aws s3 sync} skips directory marker objects
+   * (keys ending with {@code /}) when downloading, so they are never re-uploaded and are absent in
+   * the target bucket.
+   */
+  @Test
+  public void testVirtualDirectoryWithoutMarker() throws S3Exception {
+    // Set up a normal directory tree with markers and content.
+    client.createDirectory("/virtual-dir");
+    pushContent("/virtual-dir/file1", "file1");
+    client.createDirectory("/virtual-dir/sub-dir");
+    pushContent("/virtual-dir/sub-dir/file2", "file2");
+
+    // Simulate the post-sync state by deleting just the directory marker objects.
+    // deleteObjects(Collection, int) accepts raw keys, bypassing sanitizedFilePath checks.
+    client.deleteObjects(List.of("virtual-dir/", "virtual-dir/sub-dir/"), 100);
+
+    // The paths should still be considered directories via the virtual-directory fallback.
+    assertTrue(
+        "A path with objects under it should be considered a virtual directory",
+        client.isDirectory("/virtual-dir"));
+    assertTrue(
+        "A nested path with objects under it should be considered a virtual directory",
+        client.isDirectory("/virtual-dir/sub-dir"));
+
+    // A path with neither a marker nor any objects underneath must not be a directory.
+    assertFalse(
+        "A path with no objects and no marker should not be a directory",
+        client.isDirectory("/virtual-dir/empty-sub-dir"));
+  }
+
   /** Check listing objects of a directory. */
   @Test
   public void testListDir() throws S3Exception {
diff --git a/solr/solr-ref-guide/modules/deployment-guide/pages/backup-restore.adoc b/solr/solr-ref-guide/modules/deployment-guide/pages/backup-restore.adoc
index e6fa3e4d4039..5a53da952472 100644
--- a/solr/solr-ref-guide/modules/deployment-guide/pages/backup-restore.adoc
+++ b/solr/solr-ref-guide/modules/deployment-guide/pages/backup-restore.adoc
@@ -672,6 +672,14 @@ The location must already exist within your S3 bucket before you can perform any
 Empty Location::
 If you do not want to use a sub-directory within your bucket to store your backup, you can use any of the following location options: `/`, `s3:/`, `s3://`.
 However the location option is mandatory and you will receive an error when trying to perform backup operations without it.
+
+Directory Markers::
+S3 has no native concept of directories.
+The `S3BackupRepository` simulates directories by uploading zero-byte marker objects (e.g., `zk_backup/configs/myconfig/`) alongside the real backup files.
+If a backup is copied through a local filesystem and re-uploaded to S3 (for example using `aws s3 sync`), these zero-byte marker objects are typically lost because most tools translate them into real filesystem directories and do not recreate them on re-upload.
++
+Solr handles this gracefully: if the directory marker is absent, Solr falls back to listing objects by key prefix to confirm that the configset files are present before restoring them.
+A restore will still fail with a clear error only if neither the marker nor any configset files can be found at the expected location.
 ====
 
 An example configuration to enable S3 backups and restore can be seen below:
diff --git a/solr/solrj/src/java/org/apache/solr/client/solrj/impl/CloudSolrClient.java b/solr/solrj/src/java/org/apache/solr/client/solrj/impl/CloudSolrClient.java
index c9199fdafff2..9631f229553b 100644
--- a/solr/solrj/src/java/org/apache/solr/client/solrj/impl/CloudSolrClient.java
+++ b/solr/solrj/src/java/org/apache/solr/client/solrj/impl/CloudSolrClient.java
@@ -1663,6 +1663,11 @@ private CompletableFuture<DocCollection> triggerCollectionRefresh(String collect
       DocCollection cached = cacheEntry == null ? null : cacheEntry.cached;
       return CompletableFuture.completedFuture(cached);
     }
+    // Remove any already-completed future that hasn't been cleaned up by whenCompleteAsync yet.
+    // Without this, computeIfAbsent below would reuse the stale done future instead of submitting
+    // a genuinely new refresh, causing callers (e.g. stale-state retry) to observe no new
+    // ref.get().
+    collectionRefreshes.computeIfPresent(collection, (k, v) -> v.isDone() ? null : v);
     return collectionRefreshes.computeIfAbsent(
         collection,
         key -> {