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.
On Tuesday, December 14, 2021 at 7:55:51 PM UTC+1 [email protected] wrote:

> Hi,
>
> I'm struggling with a disk space issue on my laptop, running Qubes 4.0 (up 
> to date). I reached ~95% of the disk usage threshold, and no matter what I 
> do I can't get it back to the pool.
>
> Most of the disk space was allocated to a single VM (used to browse, 
> download stuff etc.) so I deleted planty of data, and then did "fstrim -a 
> -v" in the VM, expecting the disk space to be returned to the pool after a 
> while. But that didn't happen - the disk usage is still reported as ~90%, 
> but AFAIK it should be ~30%.
>
> After a while (~24H) I even tried to delete the whole VM, but that didn't 
> make any difference either.
>
> So I wonder what to do - is there something wrong with the thin 
> provisioning and the disk space is lost forever, or what? Any ideas?
>
> Tomas
>

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