FWIW I managed to solve this by booting from a Fedora USB, and running "lvconvert --repair" on the pool. So roughly this:
1) boot into Fedora Workstation USB (or any other Live USB you want
2) open the LUKS device
cryptsetup luksOpen /dev/... crypted
3) run lvscan to detect all the LVM volumes etc.
lvscan
lvs
4) deactivate everything in /dev/qubes_dom0:
cd /dev/qubes_dom0
for f in *; do lvchange -an qubes_dom0/$f; done
5) repair the pool
lvconvert --repair qubes_dom0/pool00
6) reboot into Qubes
Not sure why/how it got broken, but this returned all the missing space to the pool and everything seems to be working fine.