Sounds like you need to update the padstack all the way through the design sequence. By this I mean:
After redefining you new padstack, you need to update your footprint symbol to include it.
In symbol editor do a Tools > Padstack > Refresh if same name, or Tools > Padstack > Replace if different name.
Then its always best to purge any unused padstacks since the old one may still exist in the symbol definition.
Tools > Padstack > Modify Design Padstack will get you a pop-up menu with a Purge button, do all.
After fixing and saving you revised footprint symbol, you can then replace it onto your board.
Hope this helps.