saves with mods tends to act wonky without mods, though. At least, that's been my experience.
Normally, MODs modify the code so, yes, Saves will not perform very well in a MODified game environment.
But, in this case, SonsOLiberty is just clarifing that TIF Dev change the location of the saves.
For PC release, until version 9 was:
C:\Users\*user*\AppData\Roaming\RenPy\TheIntoxicatingFlavorEG-1525881098
From version 10 and on is:
C:\Users\*user*\AppData\Roaming\RenPy\TIF_Main_
You can copy the Save files from one location to the other by I recommend that you just start a new game.