So sorry you are dealing with these issues!
That's exactly what happened to me when my protocols were switched. A change in protocol often results in different areas of infection being hit. That means there's always the potential for herxing.
Detoxing will help a lot with this. I'm not sure what you're doing for detoxing but you need to do more - it's our only hope of reducing symptoms.
Here's a link to a thread wherein members shared what they are doing for detoxing:www.healingwell.com/community/default.aspx?f=30&m=3602759
Maybe you can add a few things to your detoxing protocol and continue to add to it.
You need to stay ahead of the killing.
Jul '14 tick bite - inadequate abx from PCP
Sept '14 met LLMD - clinical Lyme dx due to Bells Palsy/started abx (CDC positive IgM)
Feb '15 weaned off abx and started full Cowden protocol along w/LDN - 90% healed
Aug '15 started transition to Buhner's Lyme, Babesia & Bartonella protocols
Nov '15 stopped LDN - 98% healed
Aug '16 started modified Buhner Lyme/Bart protocol - 99% healed!