Ok guys, since we did not get any support, I tried stuff on my own and figured out a very dirty solution.
Remove nextcloud with package manager,
remove the nextcloud folder on the server (keep backups somewhere else),
install nextcoud 12 with package manager,
put your old config file and data (with DB, I was using sqlite which is easy: just put the owncloud.db file back in the data folder with the rest of your data) back in place. You might need to change the version number to 12.0.0 in your config file, but I don’t think so.
now the dirty stuff:
In the nextcloud install directory find and modify the Updater.php (in lib/private/) to “return true” where it would check if an update is possible:
change line 210-212, which look like this:
return isset($allowedPreviousVersions[$currentVendor][$majorMinor]) && (version_compare($oldVersion, $newVersion, '<=') || $this->config->getSystemValue('debug', false));
and you do the same for line 216-217, which look like this:
return isset($allowedPreviousVersions[$currentVendor][$majorMinor]) || isset($allowedPreviousVersions[$currentVendor][$oldVersion]);
After that, the update should just do its thing.
Remember to check the file permissions before starting the update!
When the update is done, put the original Updater.php back in place and give it the original permissions and ownership.
Hope that’s going to help some of you to update and get your instance back up again. For me it was a pain to have the instance broken for 3 weeks since I need the sync for work…