Being indexed cannot be a protection against temporary deindexing or a quarantine. Especially if the system suspects your account might be compromised.
Even when not changing the files, one could change the page to have a link or an obfuscated link to a malware site.
If not all your games were hit, you probably touched each of the quarantined games.
The criminals try everything. And I mean everything. I even saw a criminal create a thread like this one. Not kidding. Itch is infested with malware and under constant attack. Sure, it could be better. But if I can chose between all those complaint threads and seeing hacked accounts, I chose the option with less hacked accounts.
The problem is, you cannot prove who you are. Not within Itch. Even on a separate system like Discord, some hackers might have captured your Itch plus Discord accounts and try to get as much coverage on a weekend, before they get cought.
This is a wild guess, but if you have 2fa, log out and in completely, maybe that expedites the quarantine check. Or helps reduce risk of further quarantine.
I did mention that bot network as a reminder that just because people cannot imagine a reason why they would trigger the system, that does not mean that there are not plausible reasons that a system might be suspicious. And those bot networks do exist and there are pre-hacked devices sold for cheap.