"If you have my files, then in your time, I am no longer L."

Dead, or incapacitated to the point of no longer being able to fill the position, (which is worse, because it means comatose, a hostage, or brain damaged,) or some third alternative which he has not considered. He can think of nothing that would make him voluntarily retire, but there might conceivably be something.

No, he's probably dead.