Over the weekend I roughed out a composition using only VST synths in Cakewalk (something that I do all the time). Over the course of the session I saved the work several times so as not to loose my changes. The strangest thing happened when I saved the final time and closed Cakewalk. When I re-opened the file later in the day, the tracks had shuffled in some strange way. By shuffle, I don't mean the actual track order, I mean the MIDI data now appears to be out of order with the VSTs that were originally used. It looks almost as if the drums, which were recorded using Addictive Drums on track 2 is now triggering an instance of Rapture Pro which was used on track 3 and so on. Here's where it gets really strange, muting the AD track for instance will still allow the Rapture track to sound based on that data. I've got to be honest, I've never seen anything like this and really can't explain it any better. The overall project has 14 tracks, each with their own VST, and this type of behavior is seen in every track. Since this project was developing quite nicely, I have to loose the work. I realize that I can probably manually go through the project and fix it. Before doing that however, I'd like to ask if any of you have seen this happen, and is there a way to rescue the file?

I don't have an answer for your but more questions that might help you figure it out.
Are the Tracks Midi tracks with associated audio tracks or are they simple instrument tracks?
If you look at the midi part of the tracks are they feeding the correct Synth?
Are the tracks using midi channels different from each other or are they all recorded with the same midi channel?

Hello Reginald,
Some more information,
the tracks are all simple instrument tracks. Each track has it's own Vst instrument. Each track was recorded using the same Keyboard via a USB port. I used the Omni setting with regard to MIDI channel. 
This is the workflow I always use for recording Midi tracks. Nothing different. What makes it so puzzling is that I saved the progress I had made from the night before, and was able to resume work the next morning with no issue. I saved my work religously as the morning session went along, again with no problem. It's only after saving and exiting SPLAT for a period of time, and then attempting to resume working later that the issue occurred.

Sometimes the MIDI input and output assignments [EDIT- USED TO SAY "tracks"] can shift around if a midi interface or a synth is added/deleted.  Someone smarter than me may know why, but I suspect that Sonar somehow numbers the midi ins/outs within the project and when one gets added or deleted, the numbering assignments can shift around and get mangled.  Make sure you don't change any of those ins and outs after you fix it up before saving again.

BRainbow
Sometimes the MIDI input and output assignments [EDIT- USED TO SAY "tracks"] can shift around if a midi interface or a synth is added/deleted.  Someone smarter than me may know why, but I suspect that Sonar somehow numbers the midi ins/outs within the project and when one gets added or deleted, the numbering assignments can shift around and get mangled.  Make sure you don't change any of those ins and outs after you fix it up before saving again.

It seems that this is indeed what happened. I didn't even think about that detail when I described the incident, however both you and someone in the CSUG Facebook group came to the same conclusion. I had an Arturia Spark Creative Drum Controller plugged in for part of the session, which I removed on Sunday morning because it was in the way. In the words of Rosanna Roseannadana, "It's always something!" I appreciate your taking time to reply. I'll chalk this one up to "workflow improvement tips."