Deleting an Action inside of a Reference Layer will cause it to desync.

[concavepgons]

There's a bug where If you delete (or rename) an Action inside of a Reference Layer, all of the animation channels of that layer will go out of sync. This can be managed by manually right-clicking to use "Sync All Channels to Original", but it would be better if we didn't have to worry about this happening when working on a document in Moho (especially since we cannot sync them programmatically in the Lua API). This seems to have been a bug ever since version 12.5 and it is present in the latest version 14.1.

It's very easy to recreate:

1. Open a new document
2. Create a new action for the layer in the document.
2. Create a Reference Layer.
3. Delete (or rename) the Reference Layer's Action. You will now see on the timeline all of the channels go out of sync.

[Daxel]

I can reproduce that issue.

Reference layers going out of sync have always been a recurring problem. And while this specific cause is easily avoidable, I know my reference layers go out of sync frecuently for different causes and I still haven't been succesful indentifying those causes to make a proper report like you did with this one.