That's generally not a really good sign if they disappear on you. They will often times move away from the light if they're stressed or dying. It takes awhile for them to fade into nothing, so he's probably in there somewhere, though. How big was he to start? If he's gone someplace to die on you, it can seriously tax your biological filtration, so keep a very close eye on your ammonia levels.
Tell us a little about your tank as well. How long have you had it running, what are you using for lighting, what are your water parameters, etc.? BTAs are one of the easier anemones to keep, but all anemones can be tricky. I struggled with mine close to a year before I could say that it was actually doing well.
Oh, check your sump and powerheads as well. They tend to like water flow and will often times wander too close to an inlet or powerhead and get sucked in.