Session 23 | Secrets of the Mahatma Letters 

That's a very good question... and of course the answer requires an acceptance of the "saptakosha" model or "constitution" of a human... which is, the seven "layers" or "dimensions" or "bodies" that make us a complete being. Our physical body, brain, and 5 senses are all part of our physical body. Yoga philosophy (and theosophy) teach that we also have a pranic body, emotional / astral body, lower mental body, higher mental body, buddhic / intuition body, and our atmic / pure spiritual aspect. When we speak of our "soul" or our "higher self", that usually refers to the same thing... which is also known as the "higher mental" body or "vijñanamaya kosha" in some traditions. This is most likely the aspect of KH that was active during his "retreat" or "initiation" of 90 days. We don't know for sure, but it stands to reason that any of his "lower" faculties would have been dormant / resting because the adepts perform most of their work in that realm on a regular basis. That's how they send positive influence to the world, to prominent leaders, to situations... and that's largely how they communicate amongst themselves and with their higher students (although they likely use the lower mental realm as well, to transmit and receive concrete information like data, language, specific instructions). To summarize, you are right, it was very likely that his "soul consciousness" was being initiated, taught, guided, endowed with consciousness while his physical body, pranic body, emotional body, and lower mind were "asleep" back on earth.

@@newrajayoga Thank you for this dissertation on the subject. You do make it understandable and so very intereting!