diff --git a/kernel/sql/database.go b/kernel/sql/database.go
index 1f46dd6d5..35c83d946 100644
--- a/kernel/sql/database.go
+++ b/kernel/sql/database.go
@@ -64,6 +64,7 @@ func InitDatabase(forceRebuild bool) (err error) {
 	util.IncBootProgress(2, "Initializing database...")
 
 	if forceRebuild {
+		ClearQueue()
 		WaitForWritingDatabase()
 	}
 
diff --git a/kernel/sql/queue.go b/kernel/sql/queue.go
index 02e796089..c9c71cfa2 100644
--- a/kernel/sql/queue.go
+++ b/kernel/sql/queue.go
@@ -85,6 +85,12 @@ func IsEmptyQueue() bool {
 	return 1 > len(operationQueue) && !util.IsMutexLocked(&txLock)
 }
 
+func ClearQueue() {
+	upsertTreeQueueLock.Lock()
+	defer upsertTreeQueueLock.Unlock()
+	operationQueue = nil
+}
+
 func flushTreeQueue() {
 	ops := mergeUpsertTrees()
 	if 1 > len(ops) {