Had to remember my account details just to reply to this.
I am having the EXACT same issue. Just one of the controllers keeps randomly spazzing/ disappearing on me and it has been frustrating me to no end!
I have had to put up with this issue for over 2 years now and I still haven't found any solutions. goddamit HTC, we just want our overly expensive devices to function as intended.
Did you end up finding a solution?