@burnout426 Disabling sync didn't help, that wasn't the problem. Regardless,
Solved. I was reinstalling Opera and foolishly believed that "clear user settings" would actually clear user settings. I had to manually delete the whole Appdata Opera folder to force it to create an actually fresh install. After that, it stopped this ridiculous behaviour, which I still don't know the reason for.
Best posts made by tirilka
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RE: Extension changes get deleted after I restart OperaOpera for Windows