With changing the controller type in Global SMART settings to SAT, do the drives show up properly with ata-model-serialnum (instead of scsi-1234556890) for the disk naming? I also have one of the DS4486 shelves and don't use it because I couldnt get smart data and also disk naming made things more complicated because you had to make sure you knew where disks were being moved to (I think, I might be wrong on this part).
I just tested my container on unRaid, then forced upgrade, and then pulled the container on my workstation and can't reproduce the issue.
Have you tried removing the container and re-adding? As long as you don't delete the apps folder for the container, your data won't be lost.