If you try and add a secondary footprint to a schematic library symbol, CircuitStudio replaces the listing for the old footprint in the Library Component Properties dialogue. This is obviously a bug (it should add the footprint to the list of footprints models associated with that part).
What's more is that even though the new part is listed as the new only footprint associated with that schematic symbol, in reality the original footprint is still quietly the one that gets put onto your PCB when you go to use the part in a design. If you subsequently go back to the library and delete the footprint, the original footprint will magically re-appear as the only footprint model associated with your part.
I'm using CS 1.4.9