You could try removing the warped header and flattening the flange with a hammer (dead blow) on a flat surface, but it'll probably just warp again. How thick are your flanges?
My dad told me about an old 69' firebird he had that he put headers on it. The headers were made by an unrecognized manufacturer and my dad payed for it in the end. He said the driver side flange warped and didn't fit right. So he had to keep slapping on this exhaust sealing putty which would crack shortly after applying it.