Also, if you make a new faction and give it the same name as the old one, it will save over the old one.  Did this several times to tweak little details.

Edit: Guess I just scanned your post the first time and didn't see you had three factions with the same name.  That's weird...mine definitely saved over the old version.  But then I've had a few buggy problems with the synching...

I honestly don't get it why such a basic feature isn't in the game. How could they add so much costomization to the game but choose not to add something as simple and important as a "edit faction" button.

The custom units suffer largely from the same problem, in that you can't actually edit a custom unit but only create a completely new one that shares the same name. Then you have to manually retire the old verison.

I thought this was extremely stupid when I first tried out FE, and I can't believe that this problem hasn't been addressed in LH.

What's irksome is ofttimes you just want to do simple edits, like changing the factions colors because you forgot to assign them a color beyond the default.  Or change the colors because the one you wanted to use looks horrible on the world map.