Cheers, glad to hear you got it working. I don’t think there’s any problem on your end; all my flatpaks are user-installed as a Guix System user, so it didn’t cross my mind that a habitually-placed --user
flag would not work if something was installed system-wide!
You might be interested in git-annex (see the Bob use case).
It has file tracking so you can - for example - “ask” a repository at drive A where some file is, and git-annex can tell you it’s on drives C and D.
git-annex can also enforce rules like: “always have at least 3 copies of file X, and any drive will do”; “have one copy of every file at the drives in my house, and have another at the drives in my parents’ house”; or “if a file is really big, don’t store it on certain drives”.