There is a test that can be done called an ACTH stimulation (challenge) test. ACTH is the hormone that stimulates your adrenal glands to produce cortisol. They inject you with ACTH and then measure the amount of cortisol you produce in response. Without such a test, it's next to impossible to say whether a low cortisol level is due to adrenal fatigue (which mainstream medicine does not seem to believe anyway), or a deliberate reduction by the body. I do recall reading a study of cortisol in CFS in which some of the subjects had low cortisol and were given an ACTH stimulation test. Some (not all) of them had a blunted response to this test. They then did MRIs on them and found that their adrenal glands were only 2/3 the normal size. I haven't seen much more research on that, so the reason for that is speculative. Naturopathic physicians often test cortisol and DHEA which is only part of the picture because they do not do ACTH stimulation tests. The whole HPA axis thing is massively confusing and I gave up on trying to fix mine (I had low cortisol and low DHEA, I still have low DHEA but now my cortisol level seems to be random) because I always thought the viral infections were the root cause anyway.