SONAR knows almost nothing of Kontakt files beyond the location of the main DLL, e.g. "Kontakt 5.dll". SONAR remembers and restores whatever the control settings Kontakt exposes, such as the knobs and sliders and buttons we see in the UI. That's it.
All the information about where the samples are located and how they're loaded exists solely in the instrument definition (.NKI) file. SONAR knows nothing about NKIs, individual samples nor how they are used within the NKI. Repeated file-not-found messages (assuming the files aren't actually missing) indicate a problem with the instrument definition file.
Most NKIs are saved with relative paths to the sample files. By relative path, I mean relative to wherever the NKI happens to sit. Inside the NKI, it might have a pointer to "Samples\Some_File.ncw". Note that there are no clues as to where that Samples folder really is - it's
expected to be a subdirectory beneath the NKI's folder.
This is why you cannot just move an NKI without moving all the subfolders and files associated with it. As long as you move them all and preserve the directory structure, then the NKI will have no problem finding what it needs.
I'm explaining all that in hopes it might trigger a lightbulb, but you can fix the problem even if you never figure out what really caused your problem in the first place. Maybe the NKI was built with pathnames that are no longer valid. This can happen if the developer used absolute paths (a rookie mistake that does happen). It can happen if you don't preserve the file structure when you move the instrument files.
Here's the quickest solution, that doesn't require much sleuthing: load the NKI, go through the "find missing files"
dialog - and then re-save the NKI. You can save it under a new name to avoid messing with the original file, if you like. After that, your project should come up with no missing-file messages.