Updating a motherboard on unRAID is easy, assuming the board is supported.  I successfully moved from an old Gigabyte AMD motherboard, to an Asrock z77 motherboard (just a quick test to make sure everything worked on the motherboard), and then installed ESXi 5 on the z77, and virtualized unRAID.  All data and my configuration remained in tact.  Once up and running you should do a parity check (with no correction) to ensure all is good.

 

Moving Windows to another motherboard (especially with a different chipset) is another story.  You may need to do an in-place upgrade to allow windows to boot, and will likely have to install drivers for that motherboard.  The biggest gotcha here will be making sure you have windows installation media ready for after swapping the motherboard, and drivers (especially network drivers) to get you up and running.  If you don't have an optical drive in your computer there are tools for creating bootable USB sticks for Windows Vista/7/8 and Linux.  You'd also want a copy of any pertinent drivers on a usb stick, network drivers being the most important.

I just moved 2 mainbords to other cases and left the USB stick with the case.

It all works except for the fan scripts as different controllers for the temperature and other fan port numbers where the fans are on. But i can move the scripts over with the mainbords to the other unRAID install off course..

Did you notice any increase in performance?

Not really, as my 2 servers have 16 GB memory and enough processing to do the job i think.

I only found the Atom based mainbord i also have a bit slow when it was doing something already (the unRaid gui response)