I have to agree with Eric and Aristotle.
The "atom:id" element conveys a permanent, universally unique identifier for an entry or feed.
Note that says "feed", not "feed document".
An Atom Feed Document is a representation of an Atom feed, including metadata about the feed, and some or all of the entries associated with it.
That tells us that a feed *document* can be a representation of *some* of the feed. From that we can deduce that two feed documents could represent two different parts of the same feed. Since the atom:id is unique to the feed, not the feed document, both such documents should share the same id.
Regards James
