JuicieJ
SHOW ME YA MOVES!
No. Navi went back with Link to his own time at the end of OoT and left him after that. This takes place on the Child Timeline. Phantom Hourglass is on the Adult Timeline. It's not even a remote possibility.
Well, as everyone else has said, no. The theory would be a great one if Ciela didn't find out she was the Spirit of Courage. I probably would've thought of the same thing if she hadn't, to be honest. This is the type of theory I like, but it's been proven false.
Short answer: no.
Short answer: no.