I have an sonar x3e song file with about 28 44k/24bit audio only tracks in it (about 4 min long). 15 of these are live drum tracks. I went through the process of splitting them at the transients of the kick and snare to align them to the grid (using Audiosnap with crossfades enabled). Of course all of the drum tracks were split up and now play nice and tight to the metronome. When I saved the file (which normally took a few seconds to now about 5 min) the song size went from 1.3 meg to over 80 meg! When I try to reopen the song, (which took about 4 min before the drum splitting) It now takes about 20 min to get it's act in gear so that I can continue to try to mix. My 6 core AMD with 8 gig will now hang when I try to highlight a single drum track and bounce it back to a continuous file. I've had very little trouble with any of the past versions of Sonar, so this one is a real head scratcher for me. Anyone else come across something like this?

Seems the trick is to do a "save as" to a bundle file and it will release the audio snap junk. Just don't erase the original, and once it's good to go,  re save as a CWP file again as bundles have been known to go sour. 
 
 

I don't see how 24 tracks at 48/24 could possibly be 1.3MB...it's about 5MB/minute for one track-minute of mono recording at 44/16. 
 
Cactus may have a point about the transient markers but it still seems like you're dealing with really long times...hmmm...maybe try to Apply Trimming to the clips? Maybe some clips became cloned or something?
 
BTW I don't want to bring up the bundles thing again, but FWIW, no one has yet responded to my question of whether they ever loaded a bundle immediately after saving and not have it load. if it loads after saving and doesn't load later, it's an issue with the storage medium, not the bundle. The problem is that if a bundle is compromised, the project is gone so Cactus's advice of also saving as a CWP file instead of or in addition to the bundle file is well-taken.

Quick follow up - in a strange coincidence, I ran across a .bun file from 2001. It unpacked perfectly; that's the good news. The bad news is it wanted a Dreamstation DXi, Waldorf Attack, and some Anwida plug-ins. Fortunately, I had the presence of mind to have saved most of the instrument parts as audio files, and finding a reverb shouldn't be too difficult...

Anderton
I don't see how 24 tracks at 48/24 could possibly be 1.3MB...it's about 5MB/minute for one track-minute of mono recording at 44/16. 
 

This is what I wondered at first sight as well. That song should be over 500 Mb to start with.
Think it simply: 28 mono tracks / 4 minutes each = 14 stereo tracks/4 minutes each = a shortish audio CD with 14 songs.
 
Or could it be there are only a few drum clips actually recorded and the rest is done by copying/groove clipping??
In such a case, AFAIK, the actual audio is not multiplied in the audio folder (?).
Or is all the saving taking place as MP3?? That would explain the minimal file size, and perhaps also the difficulties in saving, but it's totally wrong way to go. 
 
EDIT: My bad...the OP is talking about the cwp-file, I guess??

Yes I'm just speaking of the .cwp file, not the audio included in its own folder. No groove clips, just standard tracks split at some transients. 
Thanks Anderton, Ill look into trying some additional trimming options.
Thanks Cactus Music, I'll give the "save as/bundle" option a try later tonight and see if it reduces the file size.

Yes the file size was obviously the CWP icon, not the audio folder.
I never thought I'd recomend a CWB file but after my asking questions about it in the thread I started this was one trick I saw a use for.
And it is funny how so far we have not had any solid answers about "why" bundle files are more prone to corruption.
I guess it really doesn't matter as long as we follow the advice of "those who know better" and make sure you have copies of your work saved in more than one format.
 
My current system is at least 3 copies as CWP in a containment folder with the audio folder.
And A MIDI file too.
No problem adding a CWB file to the mix but for me I'll pass..

The project icon is not the problem, the actual size of the project file is the problem. There is an issue with too many audiosnap markers being created in the project file. Once the file gets blown out, the easiest way to recover is running the project through the bundling process.
 
It has never been established bundles are "more prone to corruption." There are numerous instances of corrupted projects. However, a corrupted bundle is usually game over for the project.

I backed it up right before I did the split, so I can just go back to that version. I may just export the raw drum tracks and reimport them into a totally new song file at the same tempo and try the split function again (then reimport them back into my original file after its bounced down).  As a last ditch effort, I could do the same in another daw and just bring the consolidated edited files back into sonar.

Try scook's idea first, it will probably save you some time.