I experienced the same issue but it solved eventually so I’ve to edit this post multiple times. Here is the summary:
Qubes Manager was not running. When I started it from Qubes menu, after clicking on any VM’s settings it crashes.
When I tried to open VM settings from Qubes Menu it gives the following error:
ValueError: Invalid literal for int() with base 10:
'100663296B'
at line 33
of file /usr/bin/qubes-vm-settings.
The output of sudo journalctl -u qubesd was this:
qubesd.service: start operation timed out. Terminating.
qubesd.service: Failed with result 'timeout'.
qubesd.service: Unit process 1976 (lvm) remains running after unit stopped.
Failed to start qubesd.service - Qubes OS daemon.
qubesd.service: Scheduled restart job, restart counter is at 1.
qubesd.service. Found left-over process 1976 (lvm) in control group wile restarting unit. Ignoring.
qubes.service: This usually indicates unclean termination of a previous run, or service implement
Starting qubesd.service - Qubes OS daemon...
Started qubesd.service - Qubes OS daemon.
All the VMs in Qubes Manager were showing 0.0 MiB Disk Usage
I checked journalctl for errors and the following error is there for all VMs
ERROR: vm.sys-net Start failed: Logical Volume "vm-sys-net-private-snap" already exists in volu.....
I tried to remove this snap volume but again got error:
sudo lvremove qubes_dom0/vm-sys-net-private-snap
Check of pool qubes_dom0/vm-pool failed (status:64). Manual repair required!
Failed to update thin pool qubes_dom0/vm-pool.
Then I tried to repair the thin pool but again got error:
sudo lvconvert --repair qubes_dom0/vm-pool
Transaction id 1999 from pool "qubes_dom0/vm-pool" does not match repaired transaction id 1998 from /dev/qubes_dom0/lvol0_pmspare.
Then I followed @unman 's solution here to take backup and then change transaction id.
sudo vgcfgbackup qubes_dom0 -f /home/user/VG_backup
Edited the new file, at the section under logical_volumes->vm-pool->segment1
changed the transaction_id to 1998.
Saved the edited file.
Restored the edited data back in:
sudo vgcfgrestore qubes_dom0 -f /home/user/VG_backup
but it failed
Then used --force to restore it again and it workd
sudo vgcfgrestore qubes_dom0 -f /home/user/VG_backup --force
Activated the edited volume:
sudo lvchange -ay qubes_dom0
It took many minutes but finally it worked. Now everything is working fine. Many thanks to @unman