Try filing it flat in a vice, to try and save the coating on the rest of the surface? If that doesn't work, you may need a thicker flange if a double gasket won't work.
I have the big bore Dave Bean headers, they are quite nice, excellent workmanship. I talked to Ken a year ago about them, and he had priced new sets but the cost was over 1k, so he didn't think he could sell them on. I had the SS ceramic coated too, since the radiation off the shiney SS was too much (melted a throttle cable, throttle stuck, crikey!! that was frightening), to reduce under hood temps. Also, they hit the stock shift linkage, and I didn't want to dent the new headers to clear, so moved the pivot point. That changed the H pattern to a angular pattern....not good. Eventually went to a modified trans and side shifter.
Jerry Rude
4005R