Hmm... I'm not quite sure I'm asking the right question.
I'm not trying to manipulate save games. I'm trying to update the mods that are currently running in my save game.
For example, if you add/update a mod in Skyrim, you don't have to create a brand new character every single time. The game tries it's best to incorporate mod changes.
Judging by your response, that means that the savegame includes a copy of a lot of the basic xml config files?