So I checked, it was not unattended-upgrades. The other service files with symlinks are timesync and sshd and indeed they both link into /lib/systemd.
Then I guess the best options are either to actually add the files into the /etc/systemd/system directory (and break the separation) or to add a note on the installation instructions of this breakage. I will just not separate /opt into a different mount point. Do you know if there is anyone on the debian side working on packaging incus into backports?
Not backports yet, currently the focus is on getting all the bits in place to have Incus added to experimental, then sid, then testing so it gets properly included in the trixie release.
It’d be great to get a package in bookworm-backports but that will be a fair amount of work and can only really happen once Incus has made it into testing first.
Thanks for the info. Just as an update, moving /opt from a partition into a subfolder in / has solved all issues on my homelab machine and workstation.