PADS Logic User Guide says "A pin can be swapped with any other pin within the gate that has the same swap class number."
The ASCII (ECO) command to swap pins is "*SWPPINS* REFDES PIN1.PIN2". It doesn't have refdes info for each gate so swapping between gates is beyond the capability of Logic (looks like a topic for Bright IDeas). You'll have to do it manually. I wonder if DxD does any better?