I had a spray-in liner applied to my elky a few years ago. I was smart enough to have the tailgate & small rear panels sprayed seperatly, so I can remove them. But I had the smugglers compartment panel sealed. Now I'd like to hinge that panel. Does anyone have experience cutting thru the spray in liner without tearing it up too badly?

I would think a nice sharp carpet knife would do the trick. Or a die grinder with a 1/32" cut off wheel maybe?
I would say you are likely going to have some touching up to do.