The Skyliner has CBR as the hub. Pop/AoA line, HS line, Riviera/Epcot line all connect at CBR. You have to disembark at CBR and pick what line you want. They shutdown the Skyliner for lighting so sometimes you can’t guarantee it’s will be running in the evenings especially with the Florida weather.
You could just leave through the IG gate, get on the Skyliner to CBR , get off and get back on going the other direction back to Epcot in the middle of your Epcot day and then renter Epcot at IG.