This is why I’d like to attempt to create the boot and main RetroPie partitions as read-only to avoid any chance of anything being written to them. Then have a 3rd partition that is used for writes (configs, save games, etc.) Just not sure how to go about configuring this for RetroPie. I’ve seen some very good guides (here and here) on how to do this for the Pi in general, but nothing specific to RetroPie. I’m sure most of the concepts would carry over but there may be some things that need to be altered.
I checked out the program that InsecureSpike linked to and while good for creating/backing up Pi images, I don’t see a way to set up the 3rd partition. The only way I’ve found is from one of the guides above, but again not sure how this works with RetroPie.