System Restore is a huge help in fixing wacked out stuff that just happens from time to time.  In windows 10 they've hidden it away but just search for it under settings... and MAKE IT ACTIVE ON YOUR HARD DRIVES!
 
It was a horrible weekend.... sat down to finally do some songwriting after being semi disabled for a week and everything I brought up.... finished, in progress, ideas, backups, templates... all said:  missing plugin....   That plugin happened to be Kontakt!   I use it a LOT on EVERYTHING.  
 
Way many hours later, after exploring oooodles of possibilities... yea, I can add NEW instances and save them and THEY'll be fine!  Just not anything I've done before! Rescanning didn't help... updated Kontakt... then even Kontakt itself couldn't be found in the plugin list, although I had NO problem bringing up Kontakt outside of Sonar.  Plugin rescannings started to hang... 
 
Almost wrote a help post half a dozen times.  Finally I decided to try system restore, as it has saved my butt SEVERAL times in the past when Sheist went south... and finally was able to bring it up...it is hard to find in windows 10 (and you do have to make it active!) and went back to a restore point before 3 of MS's redistributed blah de blah update thingies and everything is back to normal...
 
System Restore... dealt with whatever happened to the dlls and who knows what...
 
btw, at first thought maybe it was caused by the early update... a bug of sorts... but went back to june's version and still had the problem.
 
 

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
 

Hi, Robert... YIKES!  That must have been a nightmare!  I was kinda freaking out as sometimes I'll write 10 ideas a week and if all of the Kontakt setups went blank...and just midi notes were left.... OY!  Huge scary possibility I NEVER considered before! I'll pe printing my audio from now on! It was also scary as it also impacted ALL my templates!  Elaborate Kontakt instrument settings/setups were just gone, with the little saying "plugin not found"!  fortunately a roll back did the trick.  
 
I have NO idea what caused my situation... indeed, I tried moving around dll's and all sorts of stuff... they were THERE in the folders... rescanned... still coming up plugin not found.... a few days of "nightmare"
 
I'm going to keep more "restore points" in the future.
 

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
 

Bob... how do you do this?  After my recent experience, I totally agree with you!   Also, is there anyway to copy the "unique plugin ID and reinsert it?  That would be way easier...but I double it is possible.
 
Your kontakt instructions have been stellar... offloading "instances" of Kontakt to the song folder makes sense... what, naming them Kontakt 1,2,3... I guess you can't save it as a multi as you can't add to it or can you and resave the multi???  
 
Steps please, oh gurubob!

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