why my account or game got flagged in the first place
Itch will usually not talk about specifics. And being flagged in this case would probably just mean, it got put on the manual review waiting queue. https://itch.io/t/4120453/unofficial-search-and-indexing-faq
And that can take weeks and longer.
Do games just automatically get de-indexed after a while when they are not updated?
No.
A few words about your game. I disagree with the tags. That's not a role playing game, nor a survival game. It is not a roguelite nor is this pixel art. It's literal pixels. You have no avatar whose role you play, and said avatar is not in a survival situation.
That's an action game. You you would want music and sounds in such a game (look up those old Tempest arcaded games) and you would want to port that onto mobile devices. For the incremental genre, shorten your numbers, do not write 20000. The name is fine. Minimalistic game or not, your game description is rather short.