If the purpose is to update the map info to be what it should be for the file (the file is already in this projection and needs correct map information assigned), then it is perfectly fine to edit the existing Map Info via Edit Header. In this case, you would not want to reproject your file. Reprojection is used to convert the map projection to another projection or datum. But it sounds like the data are already corrected (in the correct projection/datum) but the map info is incorrect or off for some reason. What I don't understand is if you are using ENVI_SETUP_HEAD and specifying the map info structure, which explicitly takes the input coordinates you give it, then why is something else reported in the Map Info? If you open the .hdr you created with a text editor, what coordinates are written to the file? Are they different than what is reported in the Map Info dialog?