Temporarily swapping drives in duo

It should not if you shut the Duo down normally, remove the two 2TB drives noting the bay each drive was in (using a Post-It note works well) then mount the two 500GB drives in the trays and install them. The two 500GB drives should have no partitions on them. (If they have been previously used/formatted, connect them to a PC and use Windows Disk Management to remove all partitions.) Once they are installed in the Duo, power it up and let it go through the set up process. You can let it default and do this on it's own. You then shut it down, restore the original 2TB drives to the trays, re-insert into their original bay and power up. It should be up and on line in a few minutes.

If you don't mind the question - why are you using the Duo to test the drives unless you are going to use them in the Duo? Using the vendor tools to test the drives as they are connected to an SATA port on the PC motherboard is the proper way to really test the drives.