How do SkeletonModification2D stacks save?

They’re stored on the Skeleton2D’s modification_stack property as a SkeletonModificationStack2D resource. Modifications you add via the inspector or code must be on this stack to persist. Editing bones directly without assigning a stack only changes the runtime pose; saving the scene doesn’t capture it.

Why does my IK setup disappear after scene reload?

You added a SkeletonModification2DLookAt or CCDIK at runtime via code but never set skeleton.modification_stack to a persisted resource. Create a SkeletonModificationStack2D resource in the project, add it to the inspector slot, then add modifications to that stack.

Can I edit modifications in tool mode?

Yes — mark your script @tool. Changes to the stack persist if you save the resource. Be careful: tool scripts run in the editor too; guard with Engine.is_editor_hint() for editor-only logic.

Fix: Godot Skeleton2D Bone Modification Not Saved

Quick answer: Create a SkeletonModificationStack2D resource, assign it to Skeleton2D.modification_stack, then add modifications to that stack. Direct runtime bone tweaks aren’t serialized.

A 2D character’s arm uses CCDIK to follow the mouse. The IK works in play but disappears as soon as you reload the scene. Modifications added directly to a Skeleton2D at runtime aren’t saved with the scene file.

How Modifications Persist

SkeletonModification2D objects (LookAt, CCDIK, FABRIK) live inside a SkeletonModificationStack2D resource. The Skeleton2D references this stack via its modification_stack property. The stack is what gets serialized when you save the scene.

Common mistake: code adds modifications via skeleton.add_child(...) or sets fields on a freshly-constructed stack that’s never assigned. The runtime pose updates; nothing persists.

The Fix

In FileSystem dock: right-click → New Resource → SkeletonModificationStack2D → save as player_ik.tres.
Select your Skeleton2D in the scene. In Inspector, drag the .tres into Modification Stack.
Open the stack resource in the Inspector. Add SkeletonModification2DCCDIK (or LookAt etc.) to the stack.
Configure bones, targets, and enable each modification.
Save the scene and the modification stack resource.

Tool Script Editing

If you want to author modifications from script while editing:

@tool
extends Skeleton2D

func _ready():
    if Engine.is_editor_hint():
        if modification_stack == null:
            modification_stack = SkeletonModificationStack2D.new()
            modification_stack.modification_count = 1
            var ik = SkeletonModification2DCCDIK.new()
            modification_stack.set_modification(0, ik)
        # Save by hitting Ctrl+S on the scene

The @tool annotation makes the script run in the editor. is_editor_hint guards keep gameplay logic out.

Verifying

Save the scene. Reload it (Project → Reload Current). The IK setup should still be active in the scene tree. Play; bone modifications work without code initialization.

“Modifications live on the stack; the stack persists. Runtime tweaks alone don’t carry over reloads.”

Author IK in the inspector against a saved .tres — runtime code can override but the persisted setup is the source of truth.