The purpose of the serrations is to provide surface roughness to ensure that your gaskets grab properly and seal properly. What's your bet that hot dip galvanizing does something similar? As long as your flange faces aren't irregular because the zinc didn't drain away properly and left "drips" which solidified on the flange faces, you're likely fine leaving well enough alone.
If you've galvanized the pipe, you're not operating under hot conditions- galvanizing loses its effectiveness completely above 400 F Serrations are much less of a concern if you can get away with soft gasket materials. So unless you've got some cold but otherwise very high pressure pipe spools, which are galvanized for external rather than internal corrosion and where the gasket faces are not exposed to corrosives, the best thing to do is likely to leave well enough alone. Hydrotest, then do a sensitive leakage test on the flanges. If they don't leak, leave them alone.
Of course if people don't care about solving problems but instead want to follow rules without understanding WHY the rules exist, you can bring in a mobile machining operation and machine new serrations onto the flange faces. That will remove the zinc and make the underlying steel subject to the corrosion you were trying to protect against by galvanizing them, but it will meet the stupid rule!
