I recently bought a hospital grade toroid isolation transformer and removed the secondary grounding wires from the chassis and outlets. However, the outlet grounds are still tied to primary ground through the chassis. No big deal. I can just use a 3 > 2 prong connector on the outlet side for my DUT. My question is should I go ahead and reconnect all of the grounding wires back to their original state? Thanks.
If you want to use the isolation transformer as intended then both secondary wires should remain free from earth. The result will be that if "one" secondary side comes in contact with earth you still have no risk of electrocution.
This also means that you are free to use 2 or 3 prong connectors and there is no need to change this. I still recommend however to mark your outlets comming from the transformer so that it is clear that neutral and live are floating with respect to earth