diff --git a/pkg/manifest/mantaray/node.go b/pkg/manifest/mantaray/node.go
index 9561c299db..437eeb460d 100644
--- a/pkg/manifest/mantaray/node.go
+++ b/pkg/manifest/mantaray/node.go
@@ -313,10 +313,26 @@ func (n *Node) Remove(ctx context.Context, path []byte, ls LoadSaver) error {
 	rest := path[len(f.prefix):]
 	if len(rest) == 0 {
 		// full path matched
+
+		// Make the ref all zeros to indicate that this node needs to re-uploaded
+		n.ref = zero32
+		// Set the refBytesSize to 32 so that unmarshall works properly
+		n.refBytesSize = len(n.ref)
+
+		// remove the fork
 		delete(n.forks, path[0])
 		return nil
 	}
-	return f.Node.Remove(ctx, rest, ls)
+	err := f.Node.Remove(ctx, rest, ls)
+	if err != nil {
+		return err
+	}
+	// Make the ref all zeros to indicate that this node needs to re-uploaded
+	n.ref = zero32
+	// Set the refBytesSize to 32 so that unmarshall works properly
+	n.refBytesSize = len(n.ref)
+
+	return nil
 }
 
 func common(a, b []byte) (c []byte) {
diff --git a/pkg/manifest/mantaray/persist.go b/pkg/manifest/mantaray/persist.go
index 9c08769a1d..2e872056e5 100644
--- a/pkg/manifest/mantaray/persist.go
+++ b/pkg/manifest/mantaray/persist.go
@@ -5,9 +5,9 @@
 package mantaray
 
 import (
+	"bytes"
 	"context"
 	"errors"
-
 	"golang.org/x/sync/errgroup"
 )
 
@@ -61,7 +61,7 @@ func (n *Node) Save(ctx context.Context, s Saver) error {
 }
 
 func (n *Node) save(ctx context.Context, s Saver) error {
-	if n != nil && n.ref != nil {
+	if n != nil && n.ref != nil && !bytes.Equal(n.ref, zero32) {
 		return nil
 	}
 	select {
diff --git a/pkg/manifest/mantaray/persist_test.go b/pkg/manifest/mantaray/persist_test.go
index 1842b84e0e..345953c941 100644
--- a/pkg/manifest/mantaray/persist_test.go
+++ b/pkg/manifest/mantaray/persist_test.go
@@ -97,6 +97,29 @@ func TestPersistRemove(t *testing.T) {
 				[]byte("img/2.png"),
 			},
 		},
+		{
+			name: "nested-prefix-is-not-collapsed",
+			toAdd: []mantaray.NodeEntry{
+				{
+					Path: []byte("index.html"),
+				},
+				{
+					Path: []byte("img/1.png"),
+				},
+				{
+					Path: []byte("img/2/test1.png"),
+				},
+				{
+					Path: []byte("img/2/test2.png"),
+				},
+				{
+					Path: []byte("robots.txt"),
+				},
+			},
+			toRemove: [][]byte{
+				[]byte("img/2/test1.png"),
+			},
+		},
 	} {
 		ctx := context.Background()
 		var ls mantaray.LoadSaver = newMockLoadSaver()
@@ -124,7 +147,6 @@ func TestPersistRemove(t *testing.T) {
 			}
 
 			ref := n.Reference()
-
 			// reload and remove
 			nn := mantaray.NewNodeRef(ref)
 			for i := 0; i < len(tc.toRemove); i++ {
@@ -134,10 +156,12 @@ func TestPersistRemove(t *testing.T) {
 					t.Fatalf("expected no error, got %v", err)
 				}
 			}
+
 			err = nn.Save(ctx, ls)
 			if err != nil {
 				t.Fatalf("expected no error, got %v", err)
 			}
+
 			ref = nn.Reference()
 
 			// reload and lookup removed node