Hello.
I have exactly the same situation - my games disappear from search every time the game page changes. The account was created about 2 years ago, there were no complaints about it (at least itch never informed me about them), there is a link back to my itch page on Patreon, I have been using 2FA for a long time... But none of this matters - today I uploaded an update to one of my games (fixed a bug in the APK) and it immediately disappeared from search.
I understand everything about moderation and malware. But I would like to hear an explanation on the question: why does quarantine NOT affect ALL accounts/games that are updated? I see many games that are updated even several times a day, and they still remain in search. It turns out that these accounts have a privileged/trusted status, right? I would like the site administration to explain how I can get this status too.