I've been having an issue where Kontakt (I'm on 6.6.1) crashes Cubase upon opening the project file. This only happens when there's a Kontakt instance with missing samples (either because samples moved or you chose to load an instrument while ignoring missing samples).
This thread perfectly describes the issue. This happened to me first when opening an old project file after I had moved some samples around, and then again after I added an instrument that I didn't have all the samples for. It's a pretty rough issue because it's hard to root cause and very slow to try different solutions with, especially if your project file is large.
In my experience, the only way to solve the issue is to disable the instance with missing samples, save, then close and re-open Cubase. You still have to deal with the missing sample issue at some point or else the crash will persist on future opens - I just renamed a random sample to get the error to go away. As it stands, Kontakt doesn't seem to play nicely with missing samples at all - maybe a bug introduced with the changes to the resolution process.