I found something over here on /mnt/disk1. A bit confused since it's a regular XFS drive and not my SSD where this used to be?
/dev/md1p1 is on /mnt/disk1 type xfs (rw,noatime,nouuid,attr2,inode64,logbufs=8,logbsize=32k,noquota)
root@server:/# ls -lash /mnt/disk1/system/docker/
total 51G
0 drwxrwxrwx 2 root root 24 Mar 14 2021 ./
0 drwxrwxrwx 4 nobody users 47 Mar 14 2021 ../
51G -rw-rw-rw- 1 nobody users 50G May 19 14:10 docker.img
root@TheSilence:/mnt/applications# ls -lash /mnt/disk1/system/libvirt/
total 1.1G
0 drwxrwxrwx 2 root root 33 Mar 14 2021 ./
0 drwxrwxrwx 4 nobody users 47 Mar 14 2021 ../
1.1G -rw-rw-rw- 1 nobody users 1.0G May 19 14:09 libvirt.img
EDIT: "cp -R /mnt/disk1/system /mnt/applications/" fixed it.
I had to manually start the docker and VM service, but they're up and running now.
I am not 100% sure if I had some non standard setup somehow previously, but I do recall trying to move things to SSDs at some point. Maybe that caused the issue.