Tim, you are correct, there is no longer a physical connection between the High Line and NEC / Main Line at ZOO.
Kevikens, The High Line track runs "through' ZOO then passes under Girard Avenue, over the Schuylkill Expy and then up through Fairmount Park via the Belmont connector where it joins the ex-RDG line at the Columbia Avenue bridge, near Montgomery Avenue. Northbound trains follow this route then up to Falls Junction where they swing across the river on the south Falls Bridge, then up through Nicetown Jct, Newtown Jct (which is no longer a junction from CSX's perspective) to the now dedicated single track on the Short Line and up to Woodbourne and West Trenton. The nightly trains between Lansdale and Greenwich Yard (C746) utilize the Blue Line connector to Septa between Nicetown and Wayne Junctions since there is no longer a connection at Newtown Junction. Trains to Abrams and west follow the Reading Main through West Falls and up the west side of the river.
Sorry to get too far OT.
Glenn