Hello Djefferson,
I'just tired to reproduce the changes you discribe with differents maners,with and without editing in library,editing only in the PCB using
Select /component/Properties/Padstack or using Setup/Padstack....
In many way we can change the stackup (add/delete Layers) of a part in the job without need to edit in librairies.
I'do not have encountered the problem you discribe.
Coul'd you explain further ?
Best regards.
Vincent.