Hi Big!
Perhaps you can fill the hole with a skylight?
You'd have to confirm, but I'm guessing it's likely a 14x14 hole same size as a skylight. You might be hurting re-sale value? Maybe keep the AC stored so you can re-install if you ever sell?
The opening is the same as your powered ceiling vent, which are standard. Should be 14.25 x 14.25 opening. Just pull the A/C install a powered vent. There should even be a 12v line run... may not be readily visible in the opening but be tucked inside the aluminum tube. Be sure to properly seal the opening.
I've removed the AC unit (to replace a seal) and suggest you use 2 people for the job. It's heavy and awkward. Remove the inside cover, the inside clamping frame, and then the AC unit will just lift off the roof. Basically just 8 screws total. The hole will need sealing and trimming. Dicor self-leveling sealant is amazing stuff. You can screw any cover you want on the hole (skylight, fan, vent, insulation, etc.) and seal the joints and screws with Dicor and be fine. That's the way the rest of the roof is sealed.