Ok, go to the Fh2 mod folder, go to levels folder and in that, go to the individual folders for each map.
You would find a ZIP called server.zip. Access it and locate the files that need to be replaced eg. AI folder, AI Pathfinding, Gamemodes and drop the map fixes into their root folders to replace them.
If in doubt, backup the map folder first, and then work on the other. Since FH2 crashes no matter what you do, and some CTDs result in unrepairable shader issues that may go as far as requiring a re-installation of vBF2, you may want to make backups of your modded files in some folder on your PC so that you needn't have to do the surgical work each time you reinstall Fh2.
Hope this was helpful