The easiest way to carry over your progress is to copy the contents of "My games/Fall from Heaven 2/Trophies" off of your computer, then do the formatting/reinstalling/whatever that you need to do, and after FfH2 is reinstalled on your computer then copy the contents of "My games/Fall from Heaven 2/Trophies" back onto your computer.
If you've already formatted and so can't copy the file (or if you aren't trying to carry over progress but rather trying to "forge" new progress) then you'd need to edit the file. As for which file to edit, I don't think there's much choice because iirc there's only one file in that location: Trophy.cfg. The thread quoted has some information about how to try to edit the file, but if you make a mistake the mod will apparently not be very forgiving - so save a backup of the file before you attempt to edit it.