IMVHO, you can run with this arrangement:
- connect two drives to the “new” mainboard
- install NethServer on “new” mainboard + drives
- do a full USB Backup of your current setup
- download latest configuration backup of your current setup
- shutdown or disconnect the current server from the networks
- full update the new installation (if not already done during install), reboot if a new kernel comes
- restore the configuration backup
- plug the usb drive
- do data restore from your latest backup
- have dinner, read a book, take a stroll, drink some nice beverage… i mean… LIVE
don’t wait so much time in front of the screen while restoring - come back when the restore ends
- enjoy the new setup.