Finally. Resque is such a PITA with Gitlab. Hopefully the upgrade script will work properly now. I have to fix quite a few bits and pieces every upgrade. Top piece of software, though.
Upgrade (4.0 -> 4.1) ran smoothly. Only thing that was missing in the upgrade guide was installing a new version of the post-receive hook, but since gitlab:check mentioned that and even provided the command to fix this, it wasn't a problem.