Save bug issue in GoG version

A few months ago I got Pillars of Eternity on GoG and was excited to play it. Until my save got wiped. Luckily I found it and fixed it continuing forward. However, the next time that happened I tried the same trick and it couldn't work. I desperately want to continue playing this after a few months of not playing. Is there a way to prevent the save loss bug in the GoG version? Or should I just gab the steam (or upcoming ps4) version?