change retroarch save folder for every emulator. Boring, but can be done
do it the file system way : change the system save folder name to a symlink pointing to a unique directory
the dirty way : sync all in all folders. THat way you're sure to have them all, despite it's messy
I could see uploading to Google Drive or something like that relatively easily with the Drive REST API if it can be used. Let's see, add targets to watch (folders/directories). Create trigger upon kill of emulators to check if files changed. [Sync CoW for good measure.] optional If changed, sync diff. I'm rather fond of the idea of diff/delta files to maintain entire directory changes so as to reduce Google Drive clutter. Create a main zip/bzip file for initial upload of directory image then create a diff/delta file to replace until it reaches a specific percentage size difference to the original in which case create new zip/bzip and upload while deleting diff/delta file. This should make it less of a hassle on all RPi units. Now, in the case that everything is already zipped, just a regular directory image would suffice with the diff/delta.