Unless they're simply planning to air it as its own episode? With no real connection to the S3 episodes that precede it?
I think back to when Firefly was on FOX, and they aired several episodes out of order. At the
end of the season (and what turned out to be the end of the show's entire run), they aired the episode that Joss Whedon had
intended to be the
pilot episode. No explanation, just how it was.
And when the series came out on DVD, Joss was able to put the episodes in their proper order, as they really should have been seen.
Unfortunately, in Bones' case, the season 2 DVD is already finished and sold, so it's not like they can add it in its proper sequence. They may have to include it as an episode all its own with the S3 box, maybe on a separate disk, with an explanation of where in the series it actually fits. *shakes head and shrugs* I dunno, what can ya do?