Kontakt 5 showing up as "missing plugin" in all my old songs system restore to the rescue!

I have had this happen a couple times in the past, but it was not caused by Sonar.  It was actually triggered by me applying maintenance to a bunch of my Native Instruments applications for Komplete 8 Ultimate - which included maintenance for Kontakt 5.
 
I believe what occurred in MY case was that somehow the internal ID for the Kontakt plugins got assigned to a different/new one, so that it appeared to Sonar as a new module.  There is no way for Sonar to have seen the new version of Kontakt as the same plugin as what had been saved in existing projects.  
 
In MY case, I was able to rebuild each Kontakt instance manually, by inserting Kontakt again, but I had to manually load in the instruments and make sure I checked midi track output midi channels against the loaded instruments in the instance to make sure Piano midi data played the Piano midi instrument.  (I changed the midi channel assignments for the loaded instruments to match the midi output channel assignments for the various instrument midi tracks in the projects.
 
I ALSO found out the hard way that any custom tweaks I had made to any instruments from the old missing instance were LOST.  Sonar did save 'state' but all of that is gone when you insert a new Kontakt instance.  Since then, anytime I tweak a loaded instrument, I save that instrument to a folder I create within that project's project folder.  That way, ANY tweaks to any project's loaded Kontakt instruments are always recoverable later, if needed, and won't affect any other project's loaded instruments.
 
Bob Bone
 

Again - I believe each plugin has/gets a unique plugin ID, and for some reason, on a couple of occasions, I have gotten bitten in the behind by Kontakt in particular, getting a new plugin ID, and therefore Sonar did not equate the Kontakt plugin it found, against the one it was looking for.
 
I highly recommend folks consider saving off any Kontakt instruments that get tweaked within a project, so that you can quickly deal with the above situation and recover in short order.  It takes a lot less time to save off a tweaked instrument to a new folder within the project folder than it does to rebuild a Kontakt instance because of a loss of the original data.
 
Bob Bone
 

I typically learn from scar tissue and painful lessons that humble me right up.
 
As an example, after I finished my very first ever computer program as a professional computer programmer, that program was ready to insert all the input fields to their correct locations in the file, and all of that.  Well, when the programming manager came to review it, he pulled it up on his screen, and then swiped his hand randomly across the entire computer keyboard.
 
Needless to say, my program INSTANTLY crashed.  I had naively believed people would always enter the data in the right format and length and type for every field, and I had ZERO edits whatsoever in the code.
 
When I explained to my mentor what happened, he said 'Make all the mistakes you can now, because THAT is how you will learn'.  BRILLIANT words I never forgot.
 
ANYWAYS, I have learned things in Kontakt and in Sonar mostly by painful lessons, that's my secret.  :)
 
You can either save the multi-racks for each instance, OR you can save each individual instrument from within each instance, OR you can do it BOTH ways.  Any way that works for you is the way to go, and keeping each set of tweaks stored within each project folder, as a sub-folder, means you will firstly always have a means of recovering those, and secondly - you will never have to worry about tweaks for this project impacting any other project, because ONLY this project will be using instruments and multi's saved in this project's folder.
 
Have fun - sorry I do not know how to recover the old plugin ID to recover from the ID changing.  Maybe someone else has some thoughts on how that could be done.
 
At least moving forward, you may have better luck.  I certainly think my saving things off in the project folder has benefited me.
 
Bob Bone