Leave the surfaces used in the mating asthey are and create new surfaces for the changes that have come up. You may hide those old surfaces used in the mating to avoid any confusion..
I am not understanding when you say "when they get pushed up into the vault". When
I hear vault I think of PDM and I don't understand why mates are lost if this is the case.
But my thought is if you had configurations of the bearings I would think it would be as simple as
RCing on the bearing in the assembly and selecting properties and selecting a different config.