This question originally appeared in the comments of the post: Making use of Multiple Sub Transforms in a main map || HL7

I'm having a similar problem trying to get PRD(1) into PV1:ReferingDoctor and PRD(2) into PV1:ConsultingDoc

Running the subtransform will populate referring doctor for the first PRD, and then the second running will delete the PV1, make a new one with only the consulting doctor populated.