I just checked mine and it's working the same as it did before I changed the head unit. I could possibly see it not playing through the new head unit, but the headphones are IR and should still work.
My vehicle is a 2004 Denali with the factory DVD player. I don't know if that makes a difference or not. I can change whether to use the stereo function or the headphones from the DVD player. On my unit, the stereo function is an FM modulator ( I guess ). I got my head unit through Crutchfield with all the adapter harnesses. If you did as well, you may want to give them a call. Hope you figure it out.