diff --git a/mfs/dir.go b/mfs/dir.go
index 219dc4cceb02..42090bc16ec9 100644
--- a/mfs/dir.go
+++ b/mfs/dir.go
@@ -336,7 +336,7 @@ func (d *Directory) Unlink(name string) error {
 }
 
 func (d *Directory) Flush() error {
-	nd, err := d.GetNode()
+	nd, err := d.getNode(true)
 	if err != nil {
 		return err
 	}
@@ -368,7 +368,7 @@ func (d *Directory) AddChild(name string, nd node.Node) error {
 	return nil
 }
 
-func (d *Directory) sync() error {
+func (d *Directory) sync(clear bool) error {
 	for name, dir := range d.childDirs {
 		nd, err := dir.GetNode()
 		if err != nil {
@@ -379,6 +379,10 @@ func (d *Directory) sync() error {
 		if err != nil {
 			return err
 		}
+
+		if clear {
+			delete(d.childDirs, name)
+		}
 	}
 
 	for name, file := range d.files {
@@ -391,6 +395,10 @@ func (d *Directory) sync() error {
 		if err != nil {
 			return err
 		}
+
+		if clear {
+			delete(d.files, name)
+		}
 	}
 
 	return nil
@@ -407,10 +415,14 @@ func (d *Directory) Path() string {
 }
 
 func (d *Directory) GetNode() (node.Node, error) {
+	return d.getNode(false)
+}
+
+func (d *Directory) getNode(clear bool) (node.Node, error) {
 	d.lock.Lock()
 	defer d.lock.Unlock()
 
-	err := d.sync()
+	err := d.sync(clear)
 	if err != nil {
 		return nil, err
 	}
diff --git a/mfs/system.go b/mfs/system.go
index fc5be0f6e2ff..6f99e9352ef7 100644
--- a/mfs/system.go
+++ b/mfs/system.go
@@ -112,12 +112,17 @@ func (kr *Root) GetValue() FSNode {
 }
 
 func (kr *Root) Flush() error {
-	nd, err := kr.GetValue().GetNode()
-	if err != nil {
+	v := kr.GetValue()
+	if err := v.Flush(); err != nil {
 		return err
 	}
 
 	if kr.repub != nil {
+		nd, err := v.GetNode()
+		if err != nil {
+			return err
+		}
+
 		kr.repub.Update(nd.Cid())
 	}
 	return nil