In case it helps, I ran into this issue where the /mnt/user/domains folder was gone with the vdisk1.img file with it for a VM. This was after an unclean shutdown (I forgot the Unraid password, needed to unplug and reset). I reluctantly started to make a new VM to replace it.
Then, through the magic of a clean reboot, it reappeared!
So, as usual, before you panic, did you turn it off and back on again?