I'll try not to spoil anything... At the "dinner party" at the end of the movie, when Starling is attached to the fridge, Paul can be seen in the background. His head looks as it does in the beginning of the party!
Actually, he doesn't put it back on place. Paul is comfortably seated in his wheelchair while the top of his skull rests on the table in the dining room. Hannibal is busy with Clarice, so he won't have time to do it either. Not only is Paul's head complete, he's also missing the tea towel Hannibal put on him.
I don't understand why Hannibal had Paul's brain on the airplane when he didn't have enough time to get anymore...I guess it could be another brain, but I don't know.
I've only seen the movie once, couldn't stomach it a second. But as I recall, there is a seen in which Hannibal wheels Paul into another room. That's when he put the napkin on his head. Some of the time discrepencies (time for an extra serving, time to put his head back together) could very well be cleared up here.