Are you referring to the VGDS that come with the scenery ?
GSX is not supposed to change any 3rd party scenery automatically, not with jetways ( which should instead be excluded from replacement at 3rd party airports ), and not with VGDS or any other parking systems. To use a GSX VGDS on a 3rd party scenery, you must place it manually, but it won't remove the one in the scenery, so it will be added to it.