Thanks for your question. Yes, indeed we have had some anecdotal evidence of people recovering using the Gupta programme, who have had a diagnosis of Lyme disease. However as you say there is a lot of controversy about this disease and it's diagnosis.
I think that the Lyme Infection, together with HHV and EBV, all seem to represent bacterial or viral infections that for some reason are likely to precipitate a chronic syndrome in some patients, i.e. ME/CFS, Fibromyalgia etc. And in my amygdala hypothesis, I account for this in that the effectiveness of the immune system may be compromised allowing opportunistic bacterial or viral infections to be retriggered.
So to summarise, these infections could be continuing because they initially triggered a long period of Post Viral Fatigue Syndrome at the start, which then leads to a trauma in the amygdala. Then the continuing trauma in the amygdala overstimulates the sympathetic nervous system (causing ME/CFS/Fibro), which compromises immune function, meaning that the body may never fully overcome these infections. However, with amygdala retraining, the body comes back to sympathetic/parasympathetic balance, the immune system strengthens, and the body is naturally able to recover from the infections. That's my theory anyway! Further research is required to validate this hypothesis.
One simple way to think about it is simply that amygdala retraining can get the body into it's optimal healing state, therefore giving it the resources to better deal with left over infections.
If anyone is reading this who works in the field of Lyme Disease, I certainly would be interested in conducting an initial pilot study on the effects of amygdala retraining on Lyme Disease patients.