Can Botox cause the brain to stop using a muscle, resulting in a permanent effect?

There is no known case of Botox or any other neurotoxins such as Xeomin or Dysport having a permanent effect on a brain-to-muscle neuro connections. When it comes to a larger muscle like masseter the idea is that with routine and repetitive injections to achieve some loss of muscle bulk/ weakness from a disuse standpoint or at least keeping the muscle weak while the toxin is active.

The neuromodulators Botox, Dysport, and Xeomin are injected directly into targeted muscles, where they block nerve signals that prompt the muscle to contract. This only affects the receptors in the muscles themselves. None of the neuromodulators get into the bloodstream or affect the brain’s signals. The brain’s signals are still sent; the message is just blocked in the muscle. With time, however, the brain may no longer send the signals, as it has been “taught” that they do not have an effect. That may be why we see effects from continued treatment last longer and longer with repeated treatments over years. Botox’s  (Xeomin, Dysport) effects are not permanent. In the masseter, they stop blocking nerve signals after about 6 months. Over time the treated muscles become a little weaker because they’re not contracting as much. Similarly, if you stop flexing your biceps and training them with weights, they’ll weaken too. A weakened muscle doesn’t do as much damage to the skin, so your Botox may last a little longer. Please consult a board-certified dermatologist who is an expert with Botox, Xeomin, and Dysport to have your masseters treated. 

Disuse atrophy is the reason the muscle has less bulk after being treated with botox.  However after the botox wears off, over time the muscle mass will return.  Sometimes doctors stretch the truth either due to a lack of understanding or the need to embellish the effect of treatment in order to entice you to have treatment.  Botox and its effects are not permanent.