You are agravating and killing the pathogens which are causing your condition ... as they become ill due to the protocol you are following, they excrete even more of the toxins which make you sick (kind of like when an ill person throws up or has diarrhea), and when they die they burst open and all the toxins inside them spill out.
These additional toxins are poisonous themselves, and they significantly add to the acidity of your inner terrain. All of this makes the body so much more sensitive to external stimuli, thus allergies are frequently the result. They will pass as your body clears out...
But you must be able to tolerate the symptoms while you detox, else you will quit the detox and relapse. So, keep it slow and easy, and drink lots and lots.