Same warning here without using any cheat. No file overwritten or edited.
Updated to 0.10.1, finished the new Lin story step with "auto resume", and done the new step in Ashley story. The warning appears since the game was saved and restarted.
Friendships: Lin 36, Kali 29, Ashley 36, Maria 29, Nadine 28, Felicity 25, Emma 25, Autumn 20.