Thank dawg you finally got a diagnosis, SW!!!
Doxy can be very hard on the intestines so if you can work in probiotics, so much the better. Giving the antibiotic with food helps, too, but avoid giving it with dairy.
We've found in the past with stubborn cases that treatment with doxy followed by 2 wks of amoxicillin can turn things around. If she was exposed after May, she may not be chronic--this might still be the acute phase of the disease. It may be, however, that she was exposed earlier and the anaplasmosis was still 'under the radar' at the time of the first test. As I understand it, false negatives are more common than false positives.
I hope Timber has turned the corner and makes a full recovery now!