Posted on: 2008-08-23 01:06:00 UTC
I took care of a High School AU that featured characters from different times (for example, one was canonically dead when another was a few years old). When the author-wraith was exorcised and the canon snapped back, the series basically restarted and the characters were returned to how they would be at that point.
Or you could separately neuralyze each character and drop each back into the canon universe at the spot their characterization most closely matches. That would take quite a long time, of course.