diff --git a/src/test/view/treeNodes/directoryTreeNode.test.ts b/src/test/view/treeNodes/directoryTreeNode.test.ts
index 3945b469b5..47fa9e5f50 100644
--- a/src/test/view/treeNodes/directoryTreeNode.test.ts
+++ b/src/test/view/treeNodes/directoryTreeNode.test.ts
@@ -206,4 +206,57 @@ describe('DirectoryTreeNode', function () {
 			assert.strictEqual(rootDir.checkboxState?.state, vscode.TreeItemCheckboxState.Unchecked);
 		});
 	});
+
+	describe('parent pointer after phantom-root pull-up', function () {
+		// When a tree has multiple top-level directories, a temporary DirectoryTreeNode
+		// with label='' (phantom root) is used to build the tree, then its children are
+		// pulled up to the actual container. If children are not re-parented, getParent()
+		// still returns the phantom DirectoryTreeNode and processCheckboxUpdates fires
+		// refresh() on an invisible node, so checkbox state never updates visually.
+
+		it('getParent() returns undefined after child is re-parented to the container', function () {
+			const container = createMockParent();
+			const phantomRoot = new DirectoryTreeNode(container, '');
+			const subDir = new DirectoryTreeNode(phantomRoot, 'src');
+
+			// Before re-parenting: parent is the phantom root DirectoryTreeNode
+			assert.ok(subDir.getParent() instanceof DirectoryTreeNode, 'sanity: should point to phantom root before re-parenting');
+
+			// Simulate the pull-up re-parenting fix applied in filesCategoryNode / pullRequestNode / commitNode
+			subDir.parent = container;
+
+			// After re-parenting: container is not a TreeNode, so getParent() returns undefined.
+			// This means the ancestor walk in processCheckboxUpdates stops here and refresh()
+			// is called on the visible subDir node, not the invisible phantom root.
+			assert.strictEqual(subDir.getParent(), undefined, 'after re-parenting, getParent() should not return the phantom root');
+		});
+
+		it('ancestor walk stops at the topmost visible directory after re-parenting', function () {
+			const container = createMockParent();
+			const phantomRoot = new DirectoryTreeNode(container, '');
+			const topDir = new DirectoryTreeNode(phantomRoot, 'cloud');
+			const subDir = new DirectoryTreeNode(topDir, 'helm');
+			const file = new MockFileNode(subDir);
+			file.checkboxState = { state: vscode.TreeItemCheckboxState.Checked };
+
+			(subDir._children as any[]).push(file);
+			topDir._children.push(subDir);
+
+			// Re-parent: simulate fix
+			topDir.parent = container;
+
+			// Walk ancestors from file, mimicking processCheckboxUpdates
+			const ancestors: TreeNode[] = [];
+			let current = file.getParent();
+			while (current instanceof DirectoryTreeNode) {
+				ancestors.push(current);
+				current = current.getParent();
+			}
+
+			// Should find subDir and topDir, but NOT the phantom root
+			assert.strictEqual(ancestors.length, 2);
+			assert.strictEqual(ancestors[0], subDir);
+			assert.strictEqual(ancestors[1], topDir);
+		});
+	});
 });
diff --git a/src/view/treeNodes/commitNode.ts b/src/view/treeNodes/commitNode.ts
index d67aa49438..ee95b34a12 100644
--- a/src/view/treeNodes/commitNode.ts
+++ b/src/view/treeNodes/commitNode.ts
@@ -111,6 +111,7 @@ export class CommitNode extends TreeNode implements vscode.TreeItem {
 			dirNode.finalize();
 			if (dirNode.label === '') {
 				// nothing on the root changed, pull children to parent
+				dirNode._children.forEach(child => { child.parent = this; });
 				result.push(...dirNode._children);
 			} else {
 				result.push(dirNode);
diff --git a/src/view/treeNodes/filesCategoryNode.ts b/src/view/treeNodes/filesCategoryNode.ts
index 189b060c22..077974c8c5 100644
--- a/src/view/treeNodes/filesCategoryNode.ts
+++ b/src/view/treeNodes/filesCategoryNode.ts
@@ -93,6 +93,7 @@ export class FilesCategoryNode extends TreeNode implements vscode.TreeItem {
 		if (dirNode.label === '') {
 			// nothing on the root changed, pull children to parent
 			this.directories = dirNode._children;
+			this.directories.forEach(child => { child.parent = this; });
 		} else {
 			this.directories = [dirNode];
 		}
diff --git a/src/view/treeNodes/pullRequestNode.ts b/src/view/treeNodes/pullRequestNode.ts
index 7bedc0cc03..f9ddf00328 100644
--- a/src/view/treeNodes/pullRequestNode.ts
+++ b/src/view/treeNodes/pullRequestNode.ts
@@ -105,6 +105,7 @@ export class PRNode extends TreeNode implements vscode.CommentingRangeProvider2
 				dirNode.finalize();
 				if (dirNode.label === '') {
 					// nothing on the root changed, pull children to parent
+					dirNode._children.forEach(child => { child.parent = this; });
 					result.push(...dirNode._children);
 				} else {
 					result.push(dirNode);