Having punch enabled does execute behavior just like this.
 
No chance you were experimenting with punch?

Ok, the plot thickens.  I re-opened the file on another computer in X2 and X3.  I get the same results - all of the tracks stop at the end of bar 6.  However, I can import each of the audio tracks to their respective tracks on the same project and they are all there.  I did not lose the actual recordings so Sonar did record everything and save it but there is something in the actual project file that is telling Sonar that there is no audio after bar 6 even though there is actual audio for more than an hour.  I'm feeling much better that everything is there, I guess I've found an odd bug that has happened more than once and I just chalked it up to user error.  I don't feel as stupid now.
 
I can work around it, but my blood pressure would certainly be better off if this was fixed.

Interesting.
 
If you have project A.cwp
And make a copy of it to Project B.cwp
Then record a track in project A.
Close project A.
Open project B.
You will not see the recording made with project A even though it is in the same folder.
 
Is it possible that you have different versions of the cwp file?

> Yes actually that did happen to me as well a long time ago, my solution was to paste everything into a brand new project (the project got corrupted somehow).
 
And this is my recommendation to you....

I took the original project, which had the audio tracks empty after bar 6, imported the original audio files (from the audio folder - same *.wav names" back into the original project - into the original tracks, and everything was fine.  I could not "lengthen" the original track files to the appropriate length, but the newly imported tracks were fine.  I can work around it, it's just an odd issue that comes up occasionally.

I wonder if closing without saving might cause this sort of behavior...

gswitz
I wonder if closing without saving might cause this sort of behavior...

It didn't in this case.  Out of habit I saved it before I noticed the issue.  Also, I think if I had closed it without saving it the audio files would not be in the "per project" audio folder.

How about making the recording... hit Stop... then Undo or ctrl+Z. That would cause the tracks to be in the Audio folder but not in the project. Just a thought.