Yes, I would probably leave all disks as normal. Now you might want to take a backup of all of your email/exchange stuff right before you shut down this time (or like you said, copy it to another disk).
I am not sure what would be easier, copy to another drive, reconfigure exchange to point there
or
Just backup before you go down, change the disk to not be independent (normal), and restore when you come back up
up to you