Are you trying to swap the pins on all instances of the schematic sheet, or only on particular instance(s)? I don't think the latter would work, because the underlying sheet would have to be different for the different instances.
Can you share the exact messages you get when you try to push the swap back the the sch?
FWIW, I haven't messed with pin or part swapping since like AD15, because at the time it was just plain broken. I'm not sure if it's gotten any better, I haven't bothered to try it since.