I thought I would make a post about this, as it’s not a very obvious thing. I’ve seen many people have controls on a display layer. If the display layer is turned to reference (“R” in the display layer next to the name of the layer), your channels will “disappear” from the channel box. It’s confusing, because they don’t disappear until you deselect a control you have active. I’ve seen many people (myself included the first time it happened) stumble around, trying to get the channels to show up again. I’ve even heard of people reinstalling Maya, which still doesn’t “fix” the problem.
Hopefully this thread is easily found in a search, if someone is pulling their hair out.