I bet you used "open in footprint editor" from the PCB editor... in which case, it will only modify the footprint in the current layout, and not in the footprint library. So when you select "update footprint", it reverts back to what's in the library, as this is what "update footprint" does - update the current footprint with the one in the library. (Which is technically an "update" only if the footprint has been modified in the library itself.)
What I suggested is to modify the footprint in the footprint editor, but you'll need to open it in the footprint editor directly, and not from the PCB editor. If you do that and save your changes, then "update footprint" will work.
The reason I suggested this workflow is so that next time you use the same footprint in another design, you'll have the modified footprint in the library.