As thierry already mentioned. You will not loose your maps as long as you make a backup of them. You can either to as theirry said, or if you really want to keep the same directory.
Just copy your terrains folder from your current FH game to a place like your desktop.
Uninstall the game from your computer completely.
Install FH again with the original installers and patchers.
Paste your maps back into the folder in the correct place.(Mirrored as what it used to be)
The only thing you really need to keep in mind is the location of the files, so they end up the same, and possibly custom meshes from the my_objects folder that the maps might need.
Otherwise it should be rather simple.