Lyme symptoms can wax and wane regardless of treatment. One day you can be super well and the next feel like you are dying. This will happen if you are treating or not. It is just the nature of lyme.
The best thing to do is treat it as a herx and detox. But, you should be detoxing on a daily basis.
www.healingwell.com/community/default.aspx?f=30&m=3602759 This thread is over a year old but it is still an example of what so many of us do for detoxing.