I also have a history of Kontakt messing up some projects, which with the help of Noel and Cakewalk staff got traced to the VS700 (and also Octa-Capture) driver crashing, thus crashing Sonar.
When researching NI forum (long time ago) I came across a "known" issue with these Roland drivers, which never got addressed properly from either side (neither NI nor Roland) - VS700 is no legacy, so no hope there from Roland ... don't think NI will care much about an issue with a legacy driver, either. Bad luck.
However, experiencing that problem (not regularly but still a couple of times in recent years) I developed some habits when using Kontakt to avoid this - and what helped a lot was to freeze Kontakt ASAP i.e.
- use several Kontakt instances just using a single instrument (instead of one with many instruments) so you can freeze/unfreeze per instrument
- freeze before you save and exit (which will avoid this fail upon project open issue you just experienced)
- maybe these days you can synth record and simply archive original Kontakt tracks for faster workaround (but that you might have to test carefully, not sure if it works as good as the other workaround)