I use Sonar 8.5 with Windows 10, Presonus AudioBox 22VSL midi interface.  Successfully record vocals, harmony and accompaniment onto isolated tracks.  There is no bleed.  Repeat... there is no bleed when I sign the work off, save it, make mp3, save it again.  Check for bleeding, save it again.  Then when I return to the work, after OS upgrade these tracks have become one track with vocals and instrumental on one audio track.  Devastating.  This has been happening for years.  Cakewalk told me I was bouncing all tracks to clips at one time.  Didn't think I was doing that, but I stopped doing that, just in case.  No fix.  Heartbroken.

Hi. I am not sure I understand how this / what is happening.
Does this happen to projects (during playback, when SONAR is open), or exports of a project (single file to play in Win Media Player)?
How do you usually work in your projects? (What's your recording process)
All the best.

Years of legacy work lost.

 
Maybe not. Check the Audio folder. All individual waves should be in there.
 
Also, be sure to empty (delete files) your Picture Cache regularly.

I record all of my vocals and instrumentals on separate tracks.  When I'm finished they are not contaminated.  Some time lapses that includes an operating system upgrade.  When I go back to the file, opening Sonar, the Vocal track is contaminated with the instrumental track.  Instrumental tracks are not contaminated.  I save all of my files as a bundle.

By contaminated, do you mean files merged (into one single file), or playing as one track?

I have never seen a mention of anything like this from anyone else, so there is likely something specific to your situation or way of working. However it's difficult to guess at what it is without more details. If you bounce all clips to a Track, then all the original clips remain. The only way to "meld" all the clips together is to bounce them using bounce to clip.
 
That said, Soens is right...even if that's the case, the original, unbounced files still exist. If you had auto-save turned on, you may be able to retrieve a session before the bounce occurred.

Don't open the .cwb (.bun) file. Open the .cwp (wrk) file instead. If you use Per-project Audio folders, all audio files are contained there. If not, look in the global Audio folder for them. You can drag them back into the project if the project clips are bad.
 
Bundle files are separate and don't affect these. They can become "damaged" over time tho.
 
Having said all that, I've had projects where audio clips were damaged by Sonar and were unrecoverable. But that's why I Save-As to a new file after so many edits.