okay so what you see is emergency dracut shell, in the shell run lvm lvscan
example you found :
$ lvm lvscan
inactive '/dev/qubes_dom0/root'
inactive '/dev/qubes_dom0/vm'
inactive '/dev/qubes_dom0/swap'
if lvm is founded and you see inactive simply active it by issuing :
lvm lvchange -a y qubes_dom0/root
lvm lvchange -a y qubes_dom0/vm
lvm lvchange -a y qubes_dom0/swap
swapon /dev/qubes_dom0/swap