abuki Strange, I fixed the issue by replacing SkeletonAnimation.Update(0); with SkeletonAnimation.AnimationState.Update(0); in one of our scripts.

Can you tell me the design difference between these methods? Which one should I be using?

There is quite a big difference. SkeletonAnimation.Update includes AnimationState.Update, but many more things.

AnimationState.Update(0) just updates the core AnimationState and triggers animation-driven callback events, but does not appy the updated animation state to the Skeleton, does not issue callbacks like UpdateLocal, UpdateWorld, UpdateComplete and does not adjust Unity-specific things like updating the Mesh.

You can also check out the SkeletonAnimation.Update(float deltaTime) source code here.

abuki I see I am using the SkeletonAnimation.Update(0); in many other scripts without problem (probably? not checked all), but now I am unsure if it's safe, and what is the correct use case?

It is in general "safe" and normal to call SkeletonAnimation.Update(0). It can however become problematic if you e.g. create hidden infinite loops through circular callbacks (A calling B calling C calling A again) or something like that. I would recommend to attach a debugger and pause in the debugger when the editor is getting stuck. Also you could have a try removing your own custom components bit by bit until the issue no longer occurs, to get a clue how the issue is triggered.

Glad to hear you've figured it out, thanks for letting us know!

abuki We have a fairly complex track setup for the main characters, playing multiple animations in different tracks. And now it looks like when on one track the animation is interrupted and mixed to another that does not have keys for the bone the previous had, the pose for the bone is kept instead of mixing to the setup pose. Which should be the correct behavior, right?

If two animations are on the same track, then mixing out an animation by starting another one will mix out the changes of this animation if there is no key in the second animation. If there are animations on lower tracks, it's not mixed to the setup pose but the lower track will show. It's the same with the empty animation, which has no keys and mixes out the preceding animation, but does not apply the setup pose (which would be strange, overriding everything on lower tracks). If you want to mix to the setup pose on higher tracks overriding lower ones, you need to set a key identical to the setup pose, and have Animation clean up disabled in the export settings (otherwise these setup-pose keys will be removed again automatically during export).

abuki Which should be the correct behavior, right?

This sentence was a bit ambiguous. What do you assume to be the correct behaviour?

Harald have Animation clean up disabled in the export settings (otherwise these setup-pose keys will be removed again automatically during export).

Or check Layered!

abuki It rises some questions, but if there is a detailed documentation for this, please give me the link, but I am unsure if I was able to find it.

See:
https://esotericsoftware.com/spine-applying-animations
More specifically:
https://esotericsoftware.com/spine-applying-animations#Tracks
https://esotericsoftware.com/spine-applying-animations#Playback
https://esotericsoftware.com/spine-applying-animations#Empty-animations

abuki What is the correct and expected behavior? After the mixing, should bone A have keys from setup or from interrupted animation1 (depending on when we started mixing)?

"Track 2 - another third animation3 that has no keys for A" is irrelevant for bone A.
If the lower tracks don't key bone A as you've mentioned, and you're mixing-out the animation on track 1 which keys bone A to an animation which does not, you should end up with the setup pose.

If this is not your result, you might have discovered a bug. Could you please describe what result you get? Unfortunately it's a bit ambiguously written.

abuki Didn't know about the Layered tick box! That sounds very useful, can you please share a more detailed info or docs link on it?

When selecting an animation in the Tree view, you have options Export and Layered.

abuki just wanted to read some more detailed info how exactly the Layeredworks.

Normally animation clean up assumes the animation is applied on top of the setup pose -- in other words, that the animation is the first one to be applied. Clean up (among other things) will delete keys at the start of the animation that are the same as the setup pose.

When an animation is applied on top of another animation, those keys that are the same as the setup pose may be needed to override the animation below. Without this Layered check box, you can't use clean up because it will delete those keys. If you check the box you can still use clean up without losing keys at the start of the animation that are identical to the setup pose.

Layered is described in the docs under Clean Up:
https://esotericsoftware.com/spine-keys#Clean-Up

Here is the tooltip for layered:

When checked, clean up will preserve more keys by assuming this animation will be applied on top of other animations

abuki Yeah, I found it, just wanted to read some more detailed info how exactly the Layeredworks.

Note that you can also always hover over items longer or hit F1 to display the tooltip.

abuki Here is code for an isolated problem, see the last lines with TODO and comments. I would like to hear your thoughts on this?

Thanks for digging deeper! Your reproduction code can be simplified by removing anything on track 1:

using Spine;
using Spine.Unity;
using UnityEngine;

public class AnimationTest : MonoBehaviour
{
    [SerializeField] private SkeletonAnimation skeletonAnimation;
    [SerializeField] private AnimationReferenceAsset animWithKey; // animation with keyed bone
    [SerializeField] private AnimationReferenceAsset animWithoutKey; // animation without keyed bone

    private void Start () {
        skeletonAnimation.AnimationState.SetAnimation(0, animWithKey, true);
        skeletonAnimation.AnimationState.Start += AnimationStateOnStart;
    }

    private void Update () {
        // remark: hit U, wait a bit and then hit T and observe the leftover applied keys of anim0WithKey
        if (Input.GetKeyDown(KeyCode.U)) {
            skeletonAnimation.AnimationState.SetAnimation(0, animWithKey, true);
        }
        if (Input.GetKeyDown(KeyCode.T)) {
            var mainTrackEntry = skeletonAnimation.AnimationState.SetAnimation(0, animWithoutKey, true);
            mainTrackEntry.MixDuration = 0; // 0.001f fixes the issue
        }
    }

    private void AnimationStateOnStart (TrackEntry trackEntry) {
        if (trackEntry.Animation == animWithoutKey.Animation) {
            skeletonAnimation.Update(0); // TODO: This is causing the problem!
                                         // When Update(0) is called, the bone stays in idleAnimation position where it was interrupted
                                         // When Update(0) is not called, the bone mix to setup position as intended
                                         // This behavior changed after spine runtime update
                                         // Update(0) is here to prevent missing heads for one frame in some specific cases, but not sure if should be needed?
        }
    }
}

The problem seems to be due to skeletonAnimation.Update(0) being called from the callback which is called from within AnimationState.SetAnimation itself. While changing animation state from within callbacks must be done carefully (see this documentation section), we'll further investigate why exactly this is causing things to go wrong.

A quick fix BTW would be to set the mix duration to a tiny value other than 0 in the following line: mainTrackEntry.MixDuration = 0.001f;