Missing audio files in SONAR X3?

Is there any way to save a project without missing any audio files?
 
I'm producing 30 min long podcast episodes. Mostly interviews and some short music clips. Each episodes contains close to 100 tracks, each with numerous clips. I save every time I complete a segment - there are few segments in each episode.

Very often, when I re-open a project on the same computer from the same location - some audio files are missing. Opening from a bundle file takes very, very long time.
 
Is there any better way?

Seems strange you are missing just some saved audio files, considering it is the same project on the same computer. Is it just random files that are missing, or a particular type (e.g. track or clip) that's missing?
 
As to a better way, I think saving and backing up the project folder is the way to go. Seems quite a few people here think this way too. I am assuming you have "per project" settings checked, so all files are saved in their own location. I certainly find this makes it easier to locate and back up projects.

Don't save as Bundle - use per project folders.
Make 1:1 Backups on a seperate hard drive (network, USB-Drive). You can use any free backup-program.
It is best to save the whole project harddrive 1:1 to another disc with a backup-software - in fact daily.
   
We digitaze thousends tapes and vinyl for thousends of customers and have projects with over 100 hours per project with thousends of clips. At the moment over 20 terrabytes.
We never had such a problem. We work with internal harddrives as well as network drives. Since over 10 years we never lost any audiofile.
Therefor Sonar is an excellent editor.
 
 

I have never experienced this either, and not sure what is happening. As your project is complex, the steps of:

• I copy one of the introductions and paste into the 1st track.
• Delete the fourth track. 
• Listen, edit, save.

should not delete anything. SONAR doesn't delete any files on you, so they should all still be on disk. Is that "save" as a bundle file or a cwp using per project audio folders?
 
Just to clarify, is the introduction clip still visible, just "empty"? If so, you can hit Shift-K and re-associate that clip to its proper wave file. As you have many clips (being saved as their own wav files), the clip names are important to keep track of to do this, but they should not be gone.
 
In your case, I would suggest "per project audio folders" rather than bundle files. Then you can also verify using Windows Explorer in the audio folder that you are seeing the moved introduction is still there (renaming the clip before the save should verify that a new file is created). If not, that is a bug.
 
As far as "project cleanup," the best method to strip out unused wav files is to do a "Save As" on the project when finished, and create a new project folder when doing so. This will save only the cwp and associated wav files to the new folder created, but should leave everything in the original folder.
 
[this is really more of an aside, and not directly related] Bundles do have the advantage of consolidating audio to an area of a disk, but otherwise are best used to collaborate on projects IMO. A magnetic disk (HDD) will write to its first available space, so saving each clip as a wav can potentially scatter them about and induce latency from seek times. From a "disk read" perspective, I tend to bounce all clips on a track to a single clip (even with silence), since it can ease HDD seek times. For SSDs, this does not apply.
 
Bundles also induced unnecessary "packing/unpacking" overhead, so unless collaborating or consolidating files, this is just adds to save/load times.

I think the missing procedure in saving files without confusion of missing files is in the response that Mettelus gave, and that is "Save As" on the project when finished, and create a new project folder". The key is "create new project folder". 
I was missing this point (option is in the saving file pop up box menu) for years and it saved a lot of headaches and missteps in saving and deleting.