I switched from EmuDeck to RetroDeck, mainly because I wanted to sync everything between multiple computers using SyncThing and EmuDeck throws data everywhere (mainly due to using Flatpaks).

I set up RetroDeck the way I wanted it and then I ran the installer for EmuDeck, choosing the option to uninstall (was a while back, my mind is hazy on the details). It actually did uninstall it, though I think I had to delete a couple directories. It was pretty cleanly uninstalled, from what I recall.

Now I only have to sync one directory for RetroDeck, which also makes backups easy. The install also feels a lot more simple.