An isolation method is described for gravel packed zones separated by at least one packer and having an auxiliary conduit passing through the packer into adjacent zones. The conduit includes at least one each of a shunt tube, flow housing, annular space, and isolation valve housing. The flow housing, the annular space, and the isolation valve housing are all annular and formed between two concentric pipes. The method includes running in an assembly of screens isolated by at least one packer with at least one auxiliary conduit extending into adjacent zones defined by the packer when the packer is subsequently set. The method also includes closing flow in said conduit to prevent flow into shunt tubes during production based on creating a flow barrier in the annular space, the flow housing, or the isolation valve housing, the shunt tubes supplying slurry through the auxiliary conduit prior to the production.