I am going to make a guess on how this should be done. Since it is probably not something that will affect enough people to be a big problem, I doubt the reps will have the time to respond.

My guess is quite simple. Just do the same conversion as you would be doing if you did not already have ARR on PS4. I believe that it has always been the case that if you buy a registration code that is good to make access to both base game and expansion(s), you can apply it to an existing account to activate expansion(s). An existing service account already has the base.

The process of conversion of PS3 to PS4 will produce a registration code that needs to be entered via the PS4 to activate both base and expansion on PS4. But if the base is already there, it will only activate the expansion. At least that is what I would hope to be the case.

Be aware though that if this is correct, the process will still completely remove all the access from PS3 on that service account. It will not just remove access to Heavensward from PS3.

This is still just a guess. I have no way to confirm it.