I haven't done a ton with xincludes in Editor, but from what I have done, I haven't edited included XML from within the referencing document. I have normally seen Editor disallow editing of the included chunks.
From a workflow perspective, wouldn't it be better for authors to edit the individual chunks rather than edit them all together within the reference doc?
The potential problem that could occur is authors may edit the included chunks for the context that they are in. This might hurt resuseability of the chunks if they become too congruous with the other includes around them.
Sorry if that wasn't much help.