My toilet was not sitting right on the closet flange. I pulled the toilet up and found out that the closet flange is flared up where the closet bolts go. I do not want to tear the whole thing apart and waste a lot of money if I can fix it myself. Does anyone have any suggestions on the best why to replace/repair it?

There are flange repair kits at home store or you can break off the bolts and install a replacement flange. They make them different for different soil pipes but this one sounds like cast so I'd use an Oatey Twist-N-Set. It drops inside the cast and then is expanded by three stainless steel bolts inside.