Have you tried the Modify Cell & Symbol Pins option in Library Manager - under the Tools menu. It is designed to allow you to make such changes.
In the Modify Cell & symbol pins i changed just the name of a zener diode pins. I kept the pin numbers as 1 and 2 like in the cell.
When i run the packager i receive this error one for each zener diode in my schematics:
ERROR: Symbol "DIODES:zener_1K_2A" of Part "DSZ018000" specified
a pin named "A". The same symbol was previously defined
on Part "DSZ001201" with this pin named "A1".
Symbols with the same name must have identical pin names
The parts that use this symbol are correctly updated in the library
I think i soved the problem by select "Delete local data, then rebuild all local library data". hope this will be useful for other users.