diff --git a/frontend/src/utils/__tests__/id-tree.test.ts b/frontend/src/utils/__tests__/id-tree.test.ts
index b1b43135122..3fb76467d8f 100644
--- a/frontend/src/utils/__tests__/id-tree.test.ts
+++ b/frontend/src/utils/__tests__/id-tree.test.ts
@@ -1991,4 +1991,52 @@ describe("CollapsibleTree.fromWithPreviousShape", () => {
     expect(tree.isCollapsed("one")).toBe(false);
     expect(tree.topLevelIds).toEqual(["one", "three", "four"]);
   });
+
+  it("reproduces GitHub issue #6188: inOrderIds with nested collapses", () => {
+    // Simplified reproduction case:
+    // Cell A (markdown): # Section 1 Header
+    // Cell B (markdown): ## Subsection 1.1 Header
+    // Cell C (python): print("This cell should be in Subsection 1.1")
+    // Cell D (python): print("This cell should also be in Subsection 1.1")
+    // Cell E (markdown): ## Subsection 1.2 Header
+    // Cell F (python): print("This cell should be in Subsection 1.2")
+
+    const originalOrder = [
+      "CellA", // # Section 1 Header
+      "CellB", // ## Subsection 1.1 Header
+      "CellC", // print("This cell should be in Subsection 1.1")
+      "CellD", // print("This cell should also be in Subsection 1.1")
+      "CellE", // ## Subsection 1.2 Header
+      "CellF", // print("This cell should be in Subsection 1.2")
+    ];
+
+    // Create notebook with one column
+    let notebook = MultiColumn.from([originalOrder]);
+
+    // Before collapsing, order should be correct
+    expect(notebook.inOrderIds).toEqual(originalOrder);
+
+    const columnId = notebook.getColumnIds()[0];
+
+    // Follow the exact reproduction steps from the GitHub issue:
+    // 1. Collapse B (subsection 1.1) - includes C, D (stops before E)
+    notebook = notebook.transform(columnId, (tree) =>
+      tree.collapse("CellB", "CellD"),
+    );
+
+    // 2. Collapse E (subsection 1.2) - includes F (to end)
+    notebook = notebook.transform(columnId, (tree) =>
+      tree.collapse("CellE", undefined),
+    );
+
+    // 3. Collapse A (section 1) - includes all the rest (B, E and their children)
+    notebook = notebook.transform(columnId, (tree) =>
+      tree.collapse("CellA", undefined),
+    );
+
+    const finalOrder = notebook.inOrderIds;
+
+    // inOrderIds now correctly preserves logical order even with nested collapses
+    expect(finalOrder).toEqual(originalOrder);
+  });
 });
diff --git a/frontend/src/utils/id-tree.tsx b/frontend/src/utils/id-tree.tsx
index a10ef2c8bc3..7d2beccbfe4 100644
--- a/frontend/src/utils/id-tree.tsx
+++ b/frontend/src/utils/id-tree.tsx
@@ -77,15 +77,17 @@ export class TreeNode<T> {
   @Memoize()
   get inOrderIds(): T[] {
     const result: T[] = [];
-    const queue = [...this.children];
 
-    while (queue.length > 0) {
-      // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
-      const node = queue.shift()!;
+    // Use depth-first traversal to preserve logical document order
+    const traverse = (node: TreeNode<T>) => {
       result.push(node.value);
+      for (const child of node.children) {
+        traverse(child);
+      }
+    };
 
-      // Add children to queue to maintain breadth-first traversal
-      queue.push(...node.children);
+    for (const child of this.children) {
+      traverse(child);
     }
 
     return result;
diff --git a/marimo/_ast/load.py b/marimo/_ast/load.py
index 87bf033005d..c3e6f77452e 100644
--- a/marimo/_ast/load.py
+++ b/marimo/_ast/load.py
@@ -187,6 +187,13 @@ def get_notebook_status(filename: str) -> LoadResult:
     return LoadResult(status="valid", notebook=notebook, contents=contents)
 
 
+FAILED_LOAD_NOTEBOOK_MESSAGE = (
+    "Static loading of notebook failed; falling back to dynamic loading. "
+    "If you can, please report this issue to the marimo team and include your notebook if possible — "
+    "https://github.com/marimo-team/marimo/issues/new?template=bug_report.yaml"
+)
+
+
 def load_app(filename: Optional[str]) -> Optional[App]:
     """Load and return app from a marimo-generated module.
 
@@ -225,10 +232,5 @@ def load_app(filename: Optional[str]) -> Optional[App]:
         # Security advantages of static load are lost here, but reasonable
         # fallback for now.
         _app = _dynamic_load(filename)
-        LOGGER.warning(
-            "Static loading of notebook failed; "
-            "falling back to dynamic loading. "
-            "If you can, please report this issue to the marimo team — "
-            "https://github.com/marimo-team/marimo/issues/new?template=bug_report.yaml"
-        )
+        LOGGER.warning(FAILED_LOAD_NOTEBOOK_MESSAGE)
         return _app