Doxy helps regular Lyme. I was on that combination. Perhaps you are herxing, which is a worsening of the symptoms while the bugs are being killed, which really is a good thing.
You can try something natural for detoxing, like activated charcoal but ask your doc first.
To my understanding, doxycycline is most useful in the very early stages of Lyme, before the bacteria have retreated behind biofilms, slimy shields they create in the body where the immune system cannot find the bacteria. Doxy does not have the ability to pierce the slimy shields to reach the bacteria, but other antibiotics do.
I have not heard of doxy and Biaxin being used together, but there is not one single correct approach to Lyme, and that goes double if you have one or more co-infections. Has your doc tested for anything other than Lyme?
I have not heard of that particular combination being used either. But there is a first time for everything.
When I was on Doxy, I felt like it was doing more harm than good. I felt awful! So I was switched. I agree with the above, Doxy is more effective in the early stages of the disease. I, personally do not see how Doxycycline could produce much of a herx. Maybe in combination with a cyst buster, such as Flagyl. But not in that particular combination. I could be wrong, but I just don't see how.
You weren't really specific in the worsening of your symptoms. Getting worse does not always indicate a herxheimer reaction! Medications come with side effects, especially at the higher doses as we are sometimes prescribed for Lyme. Does not always mean you are having a herx!!!
I have heard of others who had significant herxing on Doxy. If it's an intensification of symptoms, it more likely to be a herx than just side effects. I think your doctor's advice makes sense. Try to ride it out. Herxing usually gets better. Just remember, the intensification of symptoms means the bugs are dying. That's a good thing.