Hi Thoreau,
Welcome to our little spot on the forum!!
Is there any way for you to find out what she took, what dosage was and for how long? That would tell us a lot. If it was Doxycycline, and was less than 400 mgs, the answer would be she still has Lyme disease. There are other abx that are used though so she might have been treated appropriately - especially if she was treated by a doctor that had training through ILADS - International Lyme and Associated Diseases Society.
Lyme bacteria can never be completely removed from the body as far as we know at this time, so even if she did have good treatment that was applied quickly, it still may have managed to hide out and wait until her body was under 'just enough' stress to lower her immune system and then come back out again.
Lyme can cause dysfunction in glands and organs though too - has she had her adrenals properly tested?
And of course, there's the hormone imbalance as others have mentioned.
I do hope that you are able to get some answers from the sleep study though!! It might help unlock this mystery!
Please do let us know if we can be of further help!! And my sympathies for having to deal with your own health issues!