How can I repair and repaint a deck whose planks were caulked?
Eight months probably wouldn't be enough time for standing water to have caused much significant damage to the decking, and from the pictures it looks like it is fairly sound. Also, in that the timespan we're talking about was over the winter, it wouldn't have been a whole lot different than normal ice and snow accumulation. 

The one thing that you should check is the ledger attachment to the house. If it wasn't properly flashed, this could have been directing more water (than it would have before) down the side of the wall the deck is attached to. If it isn't flashed, you'll need to determine if the ledger was compromised since the deck was built and address that issue.

From a more practical standpoint, if there are planks that need to be replaced, you'll find them when you're doing your surface prep. I would personally remove all of the nails and replace them with quality decking screws - having popped up nail heads on an eight year old deck isn't out of the ordinary. Nails aren't ideally suited for attaching deck planks.