Hi Ulka, thanks for your compliment on my article. Unfortunately, I haven’t come across any studies or much discussion about the problem with habituation and isochronic tones and how to overcome it. The consensus among experienced users is to regularly change the frequencies and music soundtracks you listen to. Adding music to the tones does change the waveform you are stimulated with, so that’s one of the main reasons why I provide different soundtracks for my isochronic tones sessions. I have released some tracks which use amplitude modulations in the music, instead of isochronic tones. It might be worth giving them a try if you haven’t already. I have them in a playlist on YouTube https://www.youtube.com/watch?v=Lj5tHl2cuWw&list=PLveg0IEcZWN6OIRZyLkv0BJADY7Q6xFCl.
I am fortunate to be working with Deepak Chopra, M.D., and Dr. Rudy Tanzi, co-authors of the bestselling book Super Brain, on a technology called Brain Wave Entrainment. Deepak is very well known, but Rudy is an amazingly interesting person as well. He is the Kennedy Professor of Neurology at Harvard Medical School and Vice-Chair of Neurology at Mass General Hospital. Rudy co-discovered three of the four original Alzheimer's genes and today runs the Alzheimer's Genome Project. He also plays the keyboards, including, at times, for Aerosmith. He is kind of a real life "Buckaroo Banzai."
♥ ← This set of tones with the bird calls from Aotearoa is keeping me awake while I finish an essay I've been working on for the past four days. Focus beats + sounds I associate with morning = wakefulness. Still craving the bed, but at least I'm not falling asleep at my desk. Thanks myNoise, without you I'd probably be listening to music and distracted.
Other entrainment methods sometimes used include autopan modulation that moves sound in an 180º arc to create a desired tone. Harmonic box entrainment, invented by James Mann, uses a layering of binaural and monaural tones that alternate between ears, requiring headphones. Sound modulation and filtering, amplitude modulation, and pitch panning use diverse sounds to create rhythmic pulses matched to the desired brainwave frequency. 

You listen to binaural beats using headphones. In each ear, you receive sound at a slightly different frequency (often accompanied by some relaxing background sounds). If your left ear receives a 300-hertz tone and your right ear receives a 280-hertz tone, your brain will process and absorb a 10-hertz tone. That’s a very low-frequency soundwave—one you can’t actually hear. But you don’t need to hear the sound for your brain to be affected by it.
It is also possible that some people experience headaches which are almost always the result of the binaural waves. Fortunately LifeFlow can also be used without headphones, since it contains not only binaural waves but other forms as well. If you’re one of the people who suffer from headaches using entrainment, you can take off the headphones and use LifeFlow over open speakers. This usually solves the problem.

Neural oscillations are rhythmic or repetitive electrochemical activity in the brain and central nervous system. Such oscillations can be characterized by their frequency, amplitude and phase. Neural tissue can generate oscillatory activity driven by mechanisms within individual neurons, as well as by interactions between them. They may also adjust frequency to synchronize with the periodic vibration of external acoustic or visual stimuli.[3]