I came here searching for a solution to a similar problem, so I note my solution:
The “group folders” plugin was marked as unstable and was disabled by the nextcloud. So, all group folders were missing in the GUI, although still on the nc_data directory. After enabling the plugin eeryathing worked again.
Even though my problem could have been a little different - adding missing files folder to ignored files list on Windows client and then removing it from it resolved the issue for me - files were downloaded back again.