@juliank Apart from files moving between cur/, tmp/, and new/, and having their filenames changed (,S appended, iirc), there should be no other changes. Not sure if syncthing can delete moved files, but if it can't, or won't, you'll end up with duplicates fairly soon. An auto-synced git repo is probably a better option in this case.
Oh, also, if you use maildir folders, then files can move between them. Not an issue with notmuch, but with traditional maildir, that's another thing that changes.