Bolton would have to be nominated again.
The power to make recess appointments is granted to the president by Article II, Section 3 of the U.S. Constitution: "The President shall have Power to fill up all Vacancies that may happen during the Recess of the Senate, by granting Commissions which shall expire at the End of their next Session."
Yes, he could put him up for nomination and then reappoint him in a Senate recess. But I very much doubt that he would do that. From the link:
President George W. Bush has placed several judges on U.S. courts of appeals via recess appointments when Senate Democrats filibustered their confirmation proceedings. In one controversial case, Judge Charles Pickering, appointed to the Fifth Circuit U.S. Court of Appeals, chose to withdraw his name from consideration for re-nomination when his recess appointment expired.
Bolton would have less support than Pickering if Bush nominated him again.
But the question of who would replace Bolton is an interesting one. January 2007 would mean that his replacement would only have a year. Potentially much less (it is after all August and Danforth [link|http://www.msnbc.msn.com/id/6640316/|resigned] on November 22 and left office on January 20). Based on that track record, it would make sense for [link|http://www.un.int/usa/|Anne Patterson] to resume her position as Acting representative to the UN.
But we'll see.
Cheers,
Scott.