You are truely a hero!
Your solution works very well. I have tested the easyrpg player with my homemade RPG and it works, as far as I have played, without any differences compered to the windows pc version.
@BillyH If you haven't fiddled with the RA's configuration, the save files would stay alonside your ROM files, in the roms sub-folders. Once you access the file shares (\\retropie\roms), you can easily check the contents of those folder and see your save files (most of them have the .srm extension).
@Jareth247 Glad you got it working; I don't think the power switch script had anything to do with it - although the incorrect file that was causing the problem for apt could have been produced by an improper shutdown in the middle of an install operation.