This is a real frustrating problem. I'm working today and everything is going fine. Today's chore was to record about 25 short guitar pieces, none longer than 1 minute. Each bit was on its own track. I was working along fine until I noticed that some of the tracks had become empty. The graphical display of data vanished and there was no sound. As I investigated, more tracks started to vanish.
 
I had been saving after every track so they wav files are there if viewed from outside of Sonar. Sonar will no longer see those files. I can play them in other media players and DAW's, but not Sonar. I created a new project and tried to import the wav files. I can see them, Sonar sees them and says it's importing them, but after the import I'm left with an empty track.
 
I've now got a major project on hold with 50 hours of recording in the can and a film crew sitting idle. Anyone care to toss a brother a life line? Until I figure what happened and how to fix it, I'm toast.

Outside shotgun try:
 
Have you opened a fresh new project and tried to import one?
Sound like for whatever reason your project is fubared

Maybe something to do with timestamps in the wav files? Maybe they are being imported and appearing much further down the time line. There are settings for this in Preferences/File/Audio Data.
 
Cheers, Peter.
 

re-install sonar...
 

I've checked all of the above without success. Even a new Sonar project wouldn't show the files. I'm hitting the help files right now and I've sent a message to tech support. Hopefully I can get on the phone with them for some hand holding.

Can you put one of the wav files somewhere (Dropbox?) where we can look at it, try to import it etc?
 

The wav files are just fine. I can play them in any DAW but Sonar. It's almost like they've been flagged by Sonar to be ignored. I created a new project, selected import audio, selected one of the wav files and selected import. Sonar shows the import progress and completes the task, except there's nothing in the track. If I do the same thing in Mixbus it works fine. I've got to take a break, been working on this for 6 hours now and everything looks fine, but isn't. I'm willing to bet it's something simple and stupid, that's why I can't find it.  Too worked up to think clearly.

Two more suggestions:
Try dragging and dropping the wav file into a new project.
Hit shift-F (with track view having the focus) to expand view to cover all clips.
 
Good luck.
 
Cheers, Peter.

My suspicion is that Sonar embeds some sort of data tags in the files and those tags go fubar'd. Now Sonar sees that the tag is there, but can't read it and chaos ensues. I would try importing the files into something else and then saving them under new names and then import that into Sonar and see if that gets it.

I've already had a note from Cakewalk support. (thanks guys) They think I should reinstall. Since it's a 40 min drive to my recording site it will have to wait until tomorrow.  Thanks for the ideas. I really wish I could call them. Where I'm recording has no internet, so no way to communicate other than phone. There's nothing I can do but drive there, try a fix, drive home and report. Not ideal to be sure. I've already cancelled tomorrows session.