PNP, FSW with AEO or FSW with 38 occupations list, Family sponsorship...whatever may be the path, every application joins the river at medicals request stage. All these paths determine your eligibility to immigrate. Once CIC determines you are eligible and get medical request, then you can pretty much ditch other applications. Remember, all these paths are just to go to medicals stage.
i concur with koolguys thoughts here from personal experience...
i had fsw applied in sep 08 which the started processing on march 5 09
and then they started my seperate pnp app sent on jan 23 09 on may 4 09...
now on may 14 09 they sent me letter that they are withdrawing my fsw... before
sending the medical request.... so yea only one route remains active from point
of medical request