When I merge animation layers with "delete baked layers" the layers still stay there.
Just another new layer comes.
When I "delete empty layers" none of the layers gets deleted, so the Animation layers just become more crowded.
When I deleted preferences userPrefs and menuSetPrefs nothing has changed.
So.. Something that worked for me was that, i tried merging the layers separately instead of selecting all of them at once. Most of the time, this issue is caused by only one of the layers being partly corrupted.
A workaround that is merging the layers separately and finding out the corrupted layer then just duplicate it (delete the original layer) and merge it.
Also, it helps to keep the merged layer at the top till you go to the base animation layer where you can select the option to keep the merged layer in the bottom.
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