Watch it again very closely. I think that is what is called a "controlled shuffle" or something like that. Note that he always shuffles off the top, leaving the bottom card intact. The bottom card has the blue backed card, and it is that card and the rest of the deck that he finally places over the selected card. When he fans them out he makes sure to put the blue card and the one under neath it at the top of the deck when he reassembles, then when he flips over the top card, he really flops over TWO cards.
That's why at the end of the trick when he flips the blue card alone over it has changed.
The link below shows the card trick video again then explains it:
