A qube window that I was using in full-screen mode died and somehow locked up 
the gui in dom0 (totally unresponsive to keyboard & mouse input, except that 
the mouse still moved the pointer), and I had to switch to a text console 
(ctl-alt-F2) and kill xfce to force it to log out and reset the gui.
That worked, but when I logged back in, all of my qube windows (and all the 
dom0 windows I had open, including some terminal emulators) momentarily flashed 
on screen one at a time in rapid succession, then disappeared. Alt-tab doesn't 
show them.

I can, however, start new dom0 windows, e.g. terminal emulator, qube manager, 
etc, and they work properly.
xl list shows all my running qubes are still running, and I can access them 
using xl console, then within them I can use xlsclients and see that everything 
is still running. But if I try to create a new window, e.g. by running xterm, 
nothing appears.

https://github.com/QubesOS/qubes-issues/issues/3147 for an unrelated issue has 
instructions to fix invisible windows:
kill qvm-start-gui process and start it again: qvm-start-gui --all --watch &
But when I do that, all my windows just flash momentarily again, and disappear, 
same as happened when I logged back in.

Using Qubes 4.0 final release, fully updated.

Please help! How can I get my windows back?

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