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I experienced exactly the same problem.
The only solution I found is:
- make copy of the footprint
- remove/add pins
- add new cell name to the PDB
You can also make copy of the symbol, add pins and then add new symbol to the PDB but then pin assignment will be deleted and you would have to assign them manually.
You cannot modify the cell or symbol while it is referenced in PDB. You cannot simply add to the PDB another symbol with missing pins - if you do so you will loose pin assignment.