I'm not sure exactly what went wrong in your end, but searching up 'Fall of Cybertron corrupted save data' has lead to multiple people saying you should just delete your save folder.
You mentioned adding 'additional extensions for the game', maybe that might be interfering with the game itself? It should work just fine with only the crack files added, unless you're also restoring multiplayer through the ReEnergized project of course. I'd suggest re-downloading the game again by extracting the game folder from the RAR file (try adding an exception to the RAR file from your anti-virus beforehand).
I recommend checking out this Steam discussion response and see if it helps:
This seems to be a problem with many users who have both games installed because they share the same save folder.
