metaal-
I agree with the others on seeking help and wondering how this rerate could have been completed without evaluating the flanges.
As for approaches I'd explore if I were in your shoes: First, your flanges are presumably failing in the operating calc which uses the M factor, not the gasket seating calc which uses Y. The first step for me would be to find a gasket with a lower M factor. Try a GMGC (kammprofile) or CMGC (eg. Graphonic).
The second, more involved (i.e. expensive) option would be to weld buildup the flange thickness. If you can do this on the backside of the flange, great. Don't forget to check for PWHT issues and you'll have to machine the flange face to bring it back from the warpage you'll cause. Otherwise, build up the flange face side, PWHT and machine as req'd. Lots of companies can offer the onsite machining. This approach, however, will likely cause you to rework the piping or nozzles on the channel.
jt