I had a fistula from anus to skin and my surgeon did a small surgery on it. He said it would be open for a while, that what he did does not close it but makes it able to close. ?? Anyway, it took a few weeks for it to close. And since I have Crohn's and one my major symptoms is diarrhea all the time, I had problems with that passing thru there, which irritated it. It hurt and continued to do so until it healed. But it did heal, and it has been almost two years now and the fistula has not come back! Yay!
On the down side, I've had 4 major abdominal surgeries including a sub-total colectomy, all thru the same abdominal incision place, and a couple new fistulas decided to follow that scar/incision out to the skin and start draining. That started over a year ago, they've been with me ever since! The bottom one frequently closes and re-opens, and always just before it reopens the area gets red, swollen and very very sore. Then it blows, drains heavily, and eases off and closes again. The other hole just stays open and drains all the time.
Whenever I go to see my surgeon, he uses those silver nitrate sticks on them (says he's removing granulomous tissue) and I have to tell you, I'm about to refuse to let him anymore!! First, it hurts like crazy!! And it continues to hurt for days after he does it. It's basically burning tissue away, and like any burn, it hurts afterwards too. And whenever he does it, those fistulas both drain a bunch for weeks afterwards -- until that tissue builds up again and almost blocks them off, perhaps? I don't know if that's why, but it reinforces my wish to not let him do that again.
Oh yeah, and when I had those major surgeries and had this huge incision, my doc would also use the silver nitrate in the incision for the same reason, removing granulomous tissue so the wound could heal properly (had to heal open for a while rather than staple it closed) and that HURT too!
Anyway, I wanted to mention all that in order to say that no, it's not odd that you'd be hurting after your doc used silver nitrate. You're not alone, it happens to me every time too. I'd say, keep an eye on it all. If the skin turns red, starts looking swollen or they start spewing pus-looking/smelling stuff, indications of infection, then call. If you press on the skin around the area and it hurts like crazy, like maybe there's another abcess forming under there, call. But otherwise you did get burned so give it time to heal that. Your body will do so if it can!