Kind of a spoiler ahead...
So, I mentioned before that Shirtless Dean in "The Splice Girls" had the anti-possession tattoo (yay!) but not the angelic handprint (boo). Actually I can think of two good reasons why he may no longer have the handprint... well, two-and-a-half...
Lame reason: Scars DO fade over time. Maybe we just couldn't see it because its appearance has lessened... and we were focusing our attention on other things...
Better reason: The scar was perhaps not a true scar but a symbol of his connection to Castiel, the angel who "gripped [him] tight and pulled [him] from Perdition". When Castiel died/faded away, so did the Handprint.
Favorite reason: Seriously, have we had any evidence that Dean still had the Handprint after Castiel fixed Dean up at the end of "Swan Song"? Cas healed all of Dean's horrific wounds from his fight with Samifer and made him all shiny again. Much like when he was brought back from Hell, perhaps the scars he had acquired since his salvation were erased. This being (I think) the first time we have seen Dean's bare shoulder since then, this one actually kinda fits.
::Nod nod nod:: Yep, I'm gonna go with that. ::resets full episode glee::