I am using only PCB, without schematic, since I only need some pads and holes.

I've also created footprint. I can place footprint on PCB and everything is fine.

However, when I update footprint and go to my PCB document, Design -> Update components from Library, select components to update and press update, I see nothing has been updated and message: Successfully updated 0 components. But in Update from Library dialog I clearly see the difference between current and new version.

Any idea why it's not updated?