qubes-wyng-util meta-prep takes such qubes.xml backup in a distinct LVM prior of merging, and is present when rebooting in dom0 merged state. User could reinject missing qubes with qubes-wyng-util meta-recover VM_NAMES and could easily be integrated automatically from LVMs being present but unmatched from qubes being present on reboot. Even giving a choice to the user to wipe those unlinked LVMs or restore qubes settings with qubes-wyng-util meta-recover.
But to answer original OP @redmind question (let’s forget about wyng actual state and integration of dom0 under Qubes 4.1, shall we…)
I still believe it is completely sane to manually create a snapshot before doing something under dom0 (creating new VMs being out of question, as explained above)
Do action touching only dom0.
Reboot into that state. Voila.