Hmmm, I've got a truck that came with one of those in-bed reversible ball gooseneck hitches. I don't need the ball at the time and have been assuming that if I want to do a 2" body lift the ball would have to go. It's got a box frame that's bolted on top of the frame under the bed and unless that mounting could be raised the ball will be too low to attach anything to. I've figured that if I try to raise the lift with the bed I'd lose any rating that the hitch has. I'm pretty sure I wouldn't want to use it.
But I don't know a lot about those hitches. I think that it'd be OK to use a longer shanked ball and leave the hitch frame where it is. Probably I'll just leave the thing and think of it as a traction aid in the winter.