Okay, so I repeated the exact steps that I did before, only this time after compiling all of the files into the "Build-Windows" folder I attempted to run the game. It crashed on the first run just like you said it would, and created the replace_done.flag file. THEN I uploaded it to steam using the SteamPipeGUI tool. After that, the game boots properly AND the achievements work!!!! Thank you so much for taking the time to reply and help me diagnose and fix this issue!!!