In the recent update the executable file and data folder have been renamed so thats caused save files to lose. But thanks to Nice Puppies we have a solution:
I noticed that after I got the recent 0.5.1 update, all of my game settings were reset when I started up the game. I found out why. Before this update, the game's save files were saved at: "Steam\SteamApps\common\Ancient Guardian\lab_data\save". Now they are saved in a different location: "Steam\SteamApps\common\Ancient Guardian\AncientGuardian_Data\save". If you want to recover your old settings, you can simply just go into the "lab_data\save" folder and cut the two files that are in there (profile.dat and settings.dat), and paste those two files into the new location which is mentioned above. Then you can delete the "lab_data" folder because it's not needed anymore
Cheers!