First disable pairing then reprogram the remote.
I ran into the same thing. Just got an X1 box, and I programmed the remote to my TV, and then saw the part where it asks if I want it to control my sound receiver. So I did that, then realized it could not turn on my receiver with this remote, and it left me without a way to change the volume on the tv. So I just did the code for the TV again and it apparently overwrote the programming for the receiver and all was well.