Creating backups before making any changes to your system is a good habit to get into.
VM Snapshots can also be created before making any changes. Then if the changes break Whonix you can revert to the previous VM image.
Qube Manger -> System -> Backup qubes
Generally speaking the maintainers version packages are OK to install.
If you previously made changes to grub you will loose them when the maintainers version is installed. But you can always re-apply them.