Ya, I new what you meant as that's what they are called on a mixer. 

Ok Same difference, but make sure you follow each signal chain and that all the busses are therefore assigned correctly to the master. 

It can only be a signal path is not complete or you have something muted. Try routing the offending "Channel" to the master and see what happens. Remove or bypass all efxs too. 


And I don't understand what you mean by a folder? There are folders for midi soft synths but not for audio, Audio is in a audio track. I'm not sure what happens if you drop an audio clip into a synth folder??? 

I would never use layers anyways, much easier to just record a new track for each take and work with those. Layers seem to cause a lot of people problems and I can see why. 
You can always insert a few new audio tracks and drag those layers to them too. Just be careful with draging out of sync. 

So I ended up importing the missing clips into my project clip by clip from the audio file. I had to insert a new track to import them to because importing to the existing track still wouldn't play the clips. When I imported them I imported as a time  clip so they all lined up. None of the clips were muted or were the tracks in any way.(I went through everything very carefully. ) Once I got them all back and working i made 5 back up copies just in case it happens again. I removed all the Fx and wiped the board clean so I can start over. There were no Fx on the tracks that were missing. I had Fx only on the busses for them so I decided to wipe the board and create a "Raw tracks" file so I could always go back to the beginning. 

In the track view I made (audio not midi) folders for each. Ex: Track #4= Vocal folder and in the folder contain all the tracks and takes for that song. Easier for me to organize things because I can expand a folder to work on just that song and have its own set of fx and routing. 

Thanks for everyone's help. If I ever figure out what caused only a few tracks to do this I will be sure to post it.