[2021] 99% complete, all achievements gone, what do?

Originally posted by YoongZY: There's a button in the dev panel in Dev mode that reset all achievement progress if you click it.

That button only resets achievements for the game (= unique buildings will be locked again), not the Steam account.

I'm afraid I have no idea what would cause the progress in Steam achievements to be affected, but Steam support would be the only ones who can potentially help you.