If an elite has purchased an extra seat, it should be possible to split the PNR and upgrade the elite's actual seat only, for example at the gate before the last segment.

IIRC there have been cases where the extra seat has volunteered for a VDB, and more cases where a GA or FA has insisted on filling the "extra" seat. It's similar to cases where a child under two has a purchased seat, but of course *could* travel as a lap kid.