Looks like whatever Kojima was working on got canned. I doubt it was MGS related since konami wouldn't reject a new MGS so it was either something new or the rumored snatcher sequel that he was calling "devil project". They just want the man to mass produce MGS games. I wouldn't be surprised if he quit konami.
I know that's a lot of speculation on my part but he says that a year of work was rendered useless, what else could it be? Peace Walker was released a year ago so it fits.
Here's what Kojima said about the project he was working on:
"The next project will challenge a certain type of taboo," he wrote. "If I mess up, I'll probably have to leave the industry. However, I don't want to pass by avoiding that. I turn 47 this year. It's been 24 years since I started making games. Today, I got an ally who would happily support me in that risk. Although it's just one person. For a start, it's good."
"The project plan still hasn't reached a detailed level, but everything is advancing simultaneously in my head. Title, game design, story, characters, setting research, the mech that appear, casting, graphic direction, sound, beginning and ending, the major story sequences. It comes together naturally in my head."