No. And besides the apps that are on Gamr13's store, you shouldn't use the other folders unless you want to screw up system apps or other actual Retail apps. You should only use the folders if you want to temporarily keep the files there.
Either way, here's a tip. Don't bother moving folders, before you uninstall RetroArch, rename it's LOCALFOLDER folder (it's as simple as adding (Backup) to the name). Let the server rename it which might take a bit, and once that's done, uninstall it. Then install the new app, open it once so a folder is generated in LOCALFOLDER, and then copy the name of the generated folder, delete it, and rename your backed up folder.