My thought is this:
You're upgrading, not pulling rock out, treating and returning it to the same tank. You've also admitted poor maintenance, so my thought is that you might have some huge bristle worms, which you may or may not want. You might also have nothing bad. But again, you're starting a new tank, so why not hyper the rocks just to be safe? It's not going to kill beneficial bacteria and deem the rock dead. I hyper salinity treat all live rock before it goes in my tank.
Again, there's more than one way to do things in this hobby, this is just the way I handle rock.
I'd give the rocks a little scrub, even to just get some detritus build up off them which might be from lack of maintenance. I also scrub any rocks with a large build up of coralline algae, because a thick layer can actually impede the filtration of the rock. And then I'd hyper them.