It seems that the body thinks, this is how it must be. "It must not change" - and after some nice time you are again where you have been.
I would think that the state arises as a "normal homeostasis" which has become completly unnormal. (I prefer this interpretation over the defence interpretation of
@Moof which is sensible as well.)
Funnily I had 15 months where beer with a lot of hops worked quite well (15 months!).
Did she give you a schedule for slowly increasing the dose? It took me 4 months to get up to my effective dose.
There is also the possibility to restrict something that works a) on the long run for avoiding any tolerance (in accordance to
@PatJ , eg I sometimes needed to stop for one or two days drinking beer), or b) immediatly when it would induce to much change. I often want to carry on with a good effect but it get worse then.
(I don´t know much about LDN, these are more generel thoughts.)