I still wasn't able to replicate it. I'll leave the case open for now.
The %localappdata% is on windows, it is a shortcut to a folder. If you paste "%localappdata%/gain_factory/game_data_.ini" in the address bar in file explorer it should open the savefile (which is human readable). The easiest thing is to do a reset for your player nutrition. Before editing the savefile, you can put all the body parts back to 1, and in the savefile, you can set "upgrade_points_", "upgrade_points_total_", and "nutrition_points_current_" to 0.0.
If you could reply with what values these three variables have before you edit them, that would maybe give me a hint to what the issue is.