My plan to handle this is to switch my VMs to NixOS, set up NixOS with impermanence using a btrfs or zfs volume that gets backed up and wiped at every startup with another that holds persistent data that also gets backed up, and just reboot once per day.
I'm currently learning how to do impermanence in all the different ways, so this is a long goal, but Nix config + backups should handle everything.