Last time we ran into this one, we made sure as much page state as possible was pushed into the fragment portion of the URL (for bookmarkability as much as anything else).

Then when the AJAX stuff saw a version mismatch, it would wait until the user completed any operation that -wasn't- stored in the fragment and put up an "updating, gimme a sec" box, and refresh itself.

It was a hell of a lot of work but -extremely- slick (which I'm allowed to say because it wasn't me who wrote that part ;)