If you maneuver a boat with some splashing in the blocking net area right before setting the blocking net, it should chase out almost all, if not all the bass from that area. If there are only one or two small bass in with the stocker fish the loss will be low and minimal which could be accounted for by stocking some extra fish. Also in most all instances the bass behind the blocking should be or likely will be small fingerling size (3"-5") and if larger stocker fish (2"-4") are added predation should be minimal.
Also if you use the blocking net to half hardily seine the area before installing the blocking net, few if any bass should be trapped behind the blocking net.