After messing around with the filesystem files, Nextcloud needs to be told that that a change has been made to the files, so it can index the changes.

I run the Nextcloud AIO docker setup. The easiest way I’ve found to do that is to open a console in the docker container, and type:

sudo -u www-data /var/www/html/occ files:scan --all

After that, all is good to go.