OK, short update then. He planned to start in Abu Dhabi to see how he's doing, reportedly he hadn't been trainning at full still although claimed the knees were fine. Then just befor Xmas he got some bad stomach virus and reportedly had high fever for 4-5 days so decided to pass the Doha and AO too as there was not enough time to prepare properly for 5-set matches. Almugro is reported to saying Rafa's knee wasn't fine despite the public claims of the opposite.
So in short it's all a huge mystery, as expected from Tio Toni aka Team Nadal.
He is due to come back now during the South American clay swing, may be Vina del Mar, or Sao Paulo or Acapulco, we'll see. Could also be out till Monte Carlo.
Not good to hear that the knees might still be in pain. I hope he comes back soon and gets healthy again. It must be difficult for him to watch it from the sideline, the way he loves tennis. Rafa should play a lighter schedule when he comes back. I think 2-3 more Slams are possible for him if he can run properly.