While the previously linked clip was on a live server with other plugins and sidemods, I can consistently recreate it on singleplayer with only pixelmon installed, and no datapacks. Clip and log attached were even on a newly created world, with freshly regenerated configs. Notice that you can see it convert from its regular form back into a mega form after the battle has ended (right before I summon the bulbasaur look in my party, as well as while im inspecting the pokemon UI near the end). When this happens, I know the ability has broken.
New recording from singleplayer: https://clipchamp.com/watch/eg2QzMYdu87
Client log: https://mclo.gs/byghVDa
While re-testing this I've also had Pixilate remain stuck on Gardevoir after it's reverted to non-mega and stayed like that.