Good question. One thing I would be careful is that if the client reconnects and thinks all files have been deleted and it starts to delete everything on the client as well. So do backups on the client before.
Normally if you restore things from backup there is a occ-command to reset the fingerprint, I haven’t tried that so far, so I can’t say if the server “wins” per default or if conflict files are created…, there could be more details in the documentation: https://docs.nextcloud.com/server/12/admin_manual/configuration_server/occ_command.html?highlight=occ#maintenance-commands
In theory you can setup a new data folder, create the .ocdata-file and the filestructure for the users. I don’t really know how this stuff behaves. I’d run a test before (small setup, just two users, sync something, then clean out the data-folder).
@nickvergessen @jospoortvliet can you tell us how Nextcloud behaves? Or is it better to save the database and start a new setup and resync everything again manually?