The engine _does_ have at least some patching capability. It seems to load "Story/story_generated.div.osi", "Story/story.div.osi" and "Story/StoryPatch.dat" on startup, the last of which is loaded via a function called "COsiris::ApplyPatchFile". So it is (at least theoretically) possible to patch existing save files. I have no idea how to generate a patch file though.
