You may be able to use vboxctrl, but VBoxManage does what you need also:

"VBoxManage.exe" controlvm "VMName" savestate

... will save the state of a VM, and shut it down (like Windows hibernate).

Backup everything (including the machine snapshot folder, which will contain the *.SAV save state file created above).

Restore/restart VMs with:

"VBoxManage.exe" startvm "VMName"

... which will restart them from the saved state file (and then delete the file).

Have a google for "windows volume shadow copy" and you may be able to minimise the time that the VMs are down, and do the backup with them back up.