First, I would incorporate the project phase into your naming convention for the Pipe Networks.
If you are able to use the proposed pipes from one phase in another phase as existing, then do so as you've described.
If, however, you need to modify a copy of said prior phase pipe network(s), then consider exporting to LandXML, and importing into a separate Civil 3D Project, making the necessary revisions in the applicable phase of work.
My $0.02