@fengmin Sorry to the inconvenience, thanks for reporting! There was indeed no way to properly update the referenced bones and AnimationState references in SkeletonRootMotion after changing SkeletonDataAsset and calling skeletonAnimation.Initialize(true).

We have just pushed a commit which now automatically updates all references at SkeletonRootMotion automatically.

A new spine-unity 4.2 unitypackage is available for download here as usual:
https://esotericsoftware.com/spine-unity-download

From the changelog:

SkeletonRootMotion components now provide a public Initialize() method which is automatically called when calling skeletonAnimation.Initialize(true) to update the necessary skeleton references. If a different root bone shall be used, be sure to set skeletonRootMotion.rootMotionBoneName before calling skeletonAnimation.Initialize(true).

Issue ticket URL for later reference:
EsotericSoftware/spine-runtimes2575

@fengmin You can register your own components to the skeletonAnimation.OnAnimationRebuild callback to get notified when Initialize(true) invalidates e.g. your skeleton and AnimationState.

skeletonAnimation.OnAnimationRebuild -= InitializeOnRebuild;
..

protected void InitializeOnRebuild (ISkeletonAnimation animatedSkeletonComponent) {
	Initialize();
}

You can find the same code in SkeletonRootMotionBase.cs:
EsotericSoftware/spine-runtimesblob/4.2/spine-unity/Assets/Spine/Runtime/spine-unity/Components/RootMotion/SkeletonRootMotionBase.cs#L179

When using SkeletonRootMotion, I found that the skeleton will return to the initial position of the animation at the last frame of the animation.

Could you please describe that in more detail, when exactly does that happen? If it happens all the time, then root motion is not active (for whatever reasons not doing anything). Or does it revert to the initial position only once after changing your SkeletonDataAsset?

When using BoneFollower at the same time, the Follow items will flash. Is there any solution?

Could you please describe what exactly happens? It has been translated as "flash", do you mean the BoneFollower object's position is wrong for a single frame?

@fengmin Thanks for the additional info. Is your run animation three cycles long in a single animation? The issue seems to occurs only after the third cycle.

How is the GameObject transform position moving? Unfortunately the video shows the RectTransform tool active, with no RectTransform borders visible either. Could you please share a video where the Translate tool is active, so that we can see the GameObject origin moving?

@fengmin Thanks for the additional information and videos. This indeed looks strange, we have not yet encountered such an issue. Could you please send us a minimal Unity project which still shows this issue? You can send it as a zip package to contact@esotericsoftware.com, briefly mentioning this forum thread URL so that we know the context. Then we can have a look at what's going wrong.

@fengmin We have just released a bugfix for SkeletonUtilityBone updating too late (before SkeletonRootMotion moves the bone back).

A new spine-unity 4.2 unitypackage is available for download here as usual:
https://esotericsoftware.com/spine-unity-download
Please let us know whether this fixes the issue on your end as well. Thanks for reporting.

Issue ticket URL for later reference:
EsotericSoftware/spine-runtimes2582

@fengmin Glad to hear, thanks for getting back to us.