diff --git a/cmd/bd/compact.go b/cmd/bd/compact.go
index 100a4497..cbbf07fc 100644
--- a/cmd/bd/compact.go
+++ b/cmd/bd/compact.go
@@ -183,6 +183,9 @@ func runCompactSingle(ctx context.Context, compactor *compact.Compactor, store *
 		originalSize, compactedSize, savingBytes,
 		float64(savingBytes)/float64(originalSize)*100)
 	fmt.Printf("  Time: %v\n", elapsed)
+
+	// Schedule auto-flush to export changes
+	markDirtyAndScheduleFlush()
 }
 
 func runCompactAll(ctx context.Context, compactor *compact.Compactor, store *sqlite.SQLiteStorage) {
@@ -304,6 +307,11 @@ func runCompactAll(ctx context.Context, compactor *compact.Compactor, store *sql
 	if totalOriginal > 0 {
 		fmt.Printf("  Saved: %d bytes (%.1f%%)\n", totalSaved, float64(totalSaved)/float64(totalOriginal)*100)
 	}
+
+	// Schedule auto-flush to export changes
+	if successCount > 0 {
+		markDirtyAndScheduleFlush()
+	}
 }
 
 func runCompactStats(ctx context.Context, store *sqlite.SQLiteStorage) {
diff --git a/cmd/bd/rename_prefix.go b/cmd/bd/rename_prefix.go
index c7466042..6fdb9621 100644
--- a/cmd/bd/rename_prefix.go
+++ b/cmd/bd/rename_prefix.go
@@ -96,6 +96,9 @@ Example:
 			os.Exit(1)
 		}
 
+		// Schedule auto-flush to export changes
+		markDirtyAndScheduleFlush()
+
 		fmt.Printf("%s Successfully renamed prefix from %s to %s\n", green("✓"), cyan(oldPrefix), cyan(newPrefix))
 
 		if jsonOutput {
diff --git a/cmd/bd/renumber.go b/cmd/bd/renumber.go
index 08773ffa..b6ef49d3 100644
--- a/cmd/bd/renumber.go
+++ b/cmd/bd/renumber.go
@@ -127,6 +127,9 @@ Risks:
 			os.Exit(1)
 		}
 
+		// Schedule auto-flush to export changes
+		markDirtyAndScheduleFlush()
+
 		fmt.Printf("%s Successfully renumbered %d issues\n", green("✓"), len(issues))
 
 		// Count actual changes