Herbs need to be administered gently. Your body has to get used to them. You should be doing small increases and not a lot of new herbs at the same time.
So assuming you are doing that, yes you can get flares with herbs.
I always thought of it like the herbs found the lyme bugs hiding in certain spots and the herbs were chasing them out of hiding to kill them.
As long as you can function, it could be a flare. Lyme loves to come and go. Remember detoxing and eating SUPER healthy, staying stress free and getting good sleep. They are just as important medicine as the herbs.
Here is a great article on flares and herxes:
www.tiredoflyme.com/herx-vs-flare-up.html