Do you mean that you have problems if you do not keep a mod under the name Fall from Heaven 2?
All of the FfH2 modmods require the contents of the Resource folder, and by default they look for those contents in Mods/Fall from Heaven 2/Resource
You can change this by editing C:\Program Files (x86)\Firaxis Games\Sid Meier's Civilization 4\Beyond the Sword\Mods\MNAI v2.5\Resource\Civ4.thm
Code:
// *** Control Bitmap Theme file
// Set the resource
[S]resource_path "Mods/Fall from Heaven 2/Resource";[/S]
resource_path "Mods/MNAI/Resource";
// Setup common properties
[S]include "Mods/Fall from Heaven 2/Resource/Themes/Civ4/Civ4Theme.thm";[/S]
include "Mods/MNAI/Resource/Themes/Civ4/Civ4Theme.thm";
Or are you just saying that saved games won't work with mods of a different name?
I'm not sure what can be done about that. I know that you can change the mod path of worldbuilder saves, but am less sure about regular saved games.
When you open a regular saved game in Notepad++, the only part that is at all legible is "Mods\[insert mod name here]\". It seems like you ought to be able to change that part to make it compatible with a renamed mod (provided the mods are similar enough that saves would not be broken for some reason other than the name difference), but my attempts to test that so far have all resulted in Runtime Errors.