diff --git a/database_writer.cc b/database_writer.cc
index a2efa890..4a3b8667 100644
--- a/database_writer.cc
+++ b/database_writer.cc
@@ -881,6 +881,15 @@ absl::Status DatabaseReader::Read(CallGraph& call_graph1,
       .Into(&similarity_)
       .Into(&confidence_);
   ABSL_RETURN_IF_ERROR(statement.Execute());
+  if (primary_filename_ == secondary_filename_) {
+    // Both sides would be read from the same .BinExport next to the results
+    // file; one of them has necessarily been overwritten by the other.
+    return absl::FailedPreconditionError(absl::StrCat(
+        "primary and secondary BinExport files both resolve to \"",
+        JoinPath(path_, primary_filename_ + ".BinExport"),
+        "\". Results for same-named binaries need to be re-diffed and saved "
+        "again"));
+  }
 
   // Function matches
   ABSL_ASSIGN_OR_RETURN(
diff --git a/ida/main_plugin.cc b/ida/main_plugin.cc
index 2834c805..de9ebbca 100644
--- a/ida/main_plugin.cc
+++ b/ida/main_plugin.cc
@@ -223,6 +223,17 @@ absl::StatusOr<bool> ExportIdbs() {
         "same name in the same directory. Please rename or move one of the "
         "files.");
   }
+  // IDA unpacks an open database next to it. The secondary export runs in a
+  // separate IDA process, which cannot open such a database and exits without
+  // exporting. Check now instead of failing after the primary export.
+  if (const std::string unpacked =
+          ReplaceFileExtension(secondary_idb_path, ".id0");
+      FileExists(unpacked)) {
+    return absl::FailedPreconditionError(absl::StrCat(
+        "The secondary database is open in another IDA instance or was not "
+        "closed properly (found \"",
+        unpacked, "\").\nPlease close it there and try again."));
+  }
 
   LOG(INFO) << "Diffing " << Basename(primary_idb_path) << " vs "
             << Basename(secondary_idb_path);
@@ -236,6 +247,20 @@ absl::StatusOr<bool> ExportIdbs() {
   RemoveAll(secondary_temp_dir).IgnoreError();
   ABSL_RETURN_IF_ERROR(CreateDirectories(secondary_temp_dir));
 
+  // The export names end up as the "filename" column of the result file and
+  // as the names of the .BinExport files saved next to it. Same-named
+  // databases (e.g. two versions of the same binary in different directories)
+  // would overwrite each other there, so disambiguate both sides the same way
+  // the BinDiff UI does.
+  std::string primary_name =
+      ReplaceFileExtension(Basename(primary_idb_path), "");
+  const std::string secondary_name =
+      ReplaceFileExtension(Basename(secondary_idb_path), "");
+  const bool same_name = primary_name == secondary_name;
+  if (same_name) {
+    primary_name += "_primary";
+  }
+
   {
     const auto& config = config::Proto();
     auto options =
@@ -254,9 +279,8 @@ absl::StatusOr<bool> ExportIdbs() {
     std::thread export_thread(
         [&status, &exporter]() { status = exporter.Export(); });
 
-    const std::string primary_binexport = JoinPath(
-        primary_temp_dir,
-        ReplaceFileExtension(Basename(primary_idb_path), ".BinExport"));
+    const std::string primary_binexport =
+        JoinPath(primary_temp_dir, absl::StrCat(primary_name, ".BinExport"));
     idc_value_t arg = primary_binexport.c_str();
     if (qstring errbuf; !call_idc_func(
             /*result=*/nullptr, "BinExportBinary", &arg,
@@ -272,6 +296,22 @@ absl::StatusOr<bool> ExportIdbs() {
           "Export of the secondary database failed: ", status.message()));
     }
   }
+  if (same_name) {
+    // IdbExporter always names its output after the database. It ignores IDA's
+    // exit code, so a failed secondary export (e.g. the database is open in
+    // another IDA instance) only shows as a missing file, which the caller
+    // reports.
+    const std::string exported = JoinPath(
+        secondary_temp_dir, absl::StrCat(secondary_name, ".BinExport"));
+    const std::string renamed =
+        JoinPath(secondary_temp_dir,
+                 absl::StrCat(secondary_name, "_secondary.BinExport"));
+    if (FileExists(exported) &&
+        std::rename(exported.c_str(), renamed.c_str()) != 0) {
+      return absl::UnknownError(absl::StrCat(
+          "Failed to rename secondary export to \"", renamed, "\""));
+    }
+  }
   return true;
 }