The /var/lib/qubes directory is supposed to contain information pertaining to all appvms, servicevms, updates, backup data,dvmdata, qubes.xml, and vm-kernels/vm-templates, but mostly stores the icon.png files for each vm except for vm-kernels directory which has the initramfs, modules.img, and vmlinuz files as well as a modules directory.
Have you checked your journalctl log to see exactly what happened, and if it's directly related to the act of cleaning?.
Maybe someone can offer more help, but personally, I'd re-install Qubes (because I'd have no clue how to remedy the situation).