There's an Achievements.sav file in the following path: C:\Users\[your user name]\AppData\LocalLow\Anduo Games\Third Crisis
(If your Users\ folder isn't in your C: drive then you can find it by opening your Start Menu (Windows Key) and typing "Run", hit enter, and in the text box type %AppData% and it should take you to the right folder, and just click your way forward to the Third Crisis folder from there.)
Deleting it should reset your achievement progress. It worked for me, but I deleted the whole Third Crisis folder to also reset save files and Gallery unlocks. Unfortunately you can't rollback specific achievements (to my knowledge), its all or nothing.