The last time I mapped with Battlecraft 42 (back when I still played vanilla BF primarily...almost a year ago) I remember that Battlecraft would rewrite some .con files when the map was saved. I could have sworn, though, that init.con wasn't one of those files. I'm working with Battlecraft again now and if I change the classes around, save the map, test it out, start Battlecraft up again, and load the map the init.con file is back to the way it started.
It may be a different problem, though; the default init.con file messes up the classes and for some reason makes the Axis close quarters and assault classes spawn as their Allied counterparts (also, the game crashes if you select one of these classes). If it helps at all it's desert Germans vs. British.
i had this same problem while changing mod folders with my map for battlcraft, i would edit my maps in bf and load em in fh, which would totally ruin the classes, my solution what i did was to rename the tag in the init.con from "bf1942" to "FH" and take the menu/init.con from a different fh map and copy the whole list and paste it into my menu/init.con, then just put your map into the fh levels folder and load it back up in battlecraft in fh and change what teams i had, ihope that helps ya, i know it soved my problem
You can fix this easily, by copying your "good" init.con to your desktop. Open it up when you saved your level, ctrl + a, ctrl + c, then ctrl + a in BC, del, then ctrl + v, and hit save.