thank you very much for your help @tzwcfq !
I will check if other VMs are broken.
I am surprised it was so easy to break two VMs, by simply copying the files and the system doesn’t have any protection against end user mistakes, don’t understand why it’s not protected.
I’ve just checked and it didn’t break my AppVM when I’ve used up all space in my AppVM private storage.
I’m even getting a notification that the qube private space is full.
And I can boot the qube just fine even with no space available.
The problem that you had seems to happen when there is no space available in vm-pool so Qubes can’t track changes in qubes filesystem anymore and breaks some things.
You can search and read more about how LVM works.
I’m no expert so I can only give you general explanation.
LVM keep track on your changes for example when you start your vault VM the LVM will keep the vault disk image unchanged in /dev/mapper/qubes_dom0-vm--vault--private and will write all your changes separately so when you remove 10 GB file in vault the LVM used space won’t be freed by these 10 GB as LVM will still keep this change.
But if you copy 10 GB file to vault and then remove it without shutting down vault then the LVM used space will be freed by 10 GB.