When I bounce/record from tracks to an aux track then save as CWB bundle. when I open the CWB file parts of the Aux tracks are missing. I think I may be doing something wrong but I can't figure out what. lol 

Cwb's don't support aux tracks (or aome other recent featurea if I remember rightly).

The Aux is not the issues.
I have spent most of the day trying to figure this out.
Project 1: audio, Midi and AUX tracks. I can open the original CWB fine of this project version but after deleting 56 tracks and saving as an CWB file then reopen it, the project is corrupted. Missing Audio and out of sink tracks.
I tested this many times removing all midi and AUX files. and after removing the 56 tracks a and saving as a CWB file it's corrupted when being opened.
 
Project two: Just audio tracks. I can open the old version fine but after a new mix it and saved as a CWB file it opens corrupted.
 
 

Any particular reason why you're saving them as Bundles?

I have had unpredictable results using CWB files over the years, Instead I choose to use per project folders and WIN RAR to compress. I believe Midi data is not saved with CWB files either.

KPerry
Cwb's don't support aux tracks (or aome other recent featurea if I remember rightly).

Just to reiterate this, when AUX tracks were introduced they made cwp files no longer backwards compatible. The AUX tracks are specifically flagged/employed in a way that made the cwp structure change. AFAIK, the cwb format was not updated, so SONAR may not know what an AUX track is when making the bundle. Do not so casually assume it is not AUX tracks until you get an official response.

A bundle file has no real use on the same machine since it increases the overhead of opens/saves (but can be useful to strip out AS data and Region FX, IIRC).

hey folks, :)
After I create the CWB I always open it right away to make sure it worked. it has always worked until last week.
I have been using the CWB files to archive to a hard drive an well as to move projects from system to system. I record my self on 1 system and mix and review mixes on two others also depending if I have to sit by my wife, ha. then it's my laptop. ;) I create CWB because I lost my 1st 3 years of projects when I just saved the projects because there nothing in them when I opened them years later.  I'm horrible at file management and it's good advise to change up to saving projects again. If I can figure it out.
 
Thanks for the help.