Hey,
at the moment, in the /entrypoint.sh is the following line:
rsync -a --delete --exclude /config/ --exclude /data/ --exclude /custom_apps/ /usr/src/nextcloud/ /var/www/html/
Please exclude also the themes directory. We have mounted our theme from the host in /var/www/html/themes. After a pull of the images, a new version was available and the hole folder /var/www/html/themes were deleted and replaced with only the example-folder from the source files.
For example, just replace /var/www/html/themes/example
kind regards
marvin