Hi there!
It sounds like your workflow of working on the same prefab could be causing some issues.
Are you animating in the scene directly or in prefab mode?
Could you provide us the steps to your workflow that cause the issue?
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It would be best if you are able to file a bug report with a sample repro project through = Unity > Help > Report a Bug…
or
Let me know any more info you can provide here and we can investigate it.
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You can also post in this forum and discuss with other users about animation here:
2D Animation Preview Packages page-5