Here's the short version: this looks like the known "VDIs show up as snapshots" bug, and you haven't done anything wrong.
What happens is a metadata flag on the VDI, is-a-snapshot, gets flipped to true after some of the recent 8.3 host updates, so XO (both 5 and 6) thinks those disks are snapshots and hides them from the per-VM Disks tab, even though the VDIs are fine and xe / XCP-ng Center still show them.
A few older threads track the same thing, the main one is https://xcp-ng.org/forum/topic/11715/vdi-not-showing-in-xo-5-from-source . From what's said there, the fix is expected in two parts: stopping it from happening again, and a way to repair the flag on VDIs that are already affected.
I don't have a timeline and could be off on the details, so please don't take that as official.
In the meantime people have made the disks reappear by migrating the affected VDI to another SR, or snapshot then revert then delete the snapshot, but it's a visual fix and can come back.
The VDI_IN_USE you're now hitting on start does sound worth its own detailed report, so yes please file it with the xapi/sm versions and that malformed is-a-snapshot field, and it'd be good to loop in @Team-Storage. Sorry you're stuck on this.
