Testing for Lyme in the later stages is difficult. The testing itself requires considerable skill in the lab doing the testing. It also requires skill and understanding of the doc, who must know what to tests to do. It is complicated.
I 'll also add that a considerable number of docs refuse to treat for Lyme until test results show Lyme. That is too late. By the time their test results are in, the 1st stage is over and damage is being done. The treatment is now much tougher. The reason given for the delay is, "to prevent the proliferation of antibiotic resistant strains of bugs". That's BS, the lesion is proof of a bacterial cause.
Your post says the problem persists. That means the bugs are still present. She should w/o question receive the appropriate antibiotic treatment to get rid of them. If her doc hasn't done this, she absolutely needs a new one. I suggest an immunologist. I haven't gone into details, but they would be the ones most likely to have the knowledge and understanding to determine exactly what's going on. By immunologist, I don't mean one of those allergy morons. If the doc starts testing for allergies, that's the clue the docs NG. He should be testing for things like elevated IgM, and heart, liver and brain problems. A GP could do this, but it's unlikely one would find one that has, or would spend the time to know and understand the important aspects involved.