@fepitre: this is what qubes-wyng-util meta-prep takes care of in such case, having a backup of qubes.xml in a different LVM which is also taken cared into a backup session, so that one can reinject missing qubes with qubes-wyng-util meta-recover VM_NAMES.
@maramek I’m interested into those problems, if you could point to other issues/discussions.
As pointed before, those are the filesystem areas that changes between dom0 reboots:
So I guess we are talking about incoherent states that could affect the system, kept under: