The game habitually removes your progress or refuses to save progress, resulting in lost progression.
You have been warned.
Apparently fixed with the v1.1.5 (for Windows) and v1.1.51 (for Mac & Linux) updates in Dec 2015.
In the last post in the "Achievements don't save after closing game" thread, Vess07 reports still getting the problem after that patch, but it seems likely to be an isolated issue on his/her system, since the mass reports of progress loss have ceased on both GOG and Steam since the update.
Unfortunately, I can't confirm one way or the other from my own experience, because I'm just doing pre-purchase investigation. ^_^