Will hypnosis work if I fall asleep?
The short answer is no. The reason is that we need your brain to be processing language for the hypnosis to have its effect, and this doesn't happen when you are asleep. However, it is entirely possible to think you have been asleep after listening to a download, when in fact you have simply got amnesia for the download content, which is fairly common.
The best way to tell whether you were truly asleep while listening to a download is whether you wake up when asked to by the narrator. With practice, you will be able to modulate your own depth of trance to ensure you stay awake; plus you will become adept at knowing afterwards whether you were asleep or not. Typically, a hypnotic trance will leave you feeling energized afterwards, while falling into the sleep state will leave you feeling groggy.
If you are having problems staying awake while listening to your download, then try listening to it sitting up. If this still doesn't work, then it may be a signal that you are sleep deprived, in which case your first priority is to get more sleep!