I have used Kontakt since v.2 but I rarely seen this problem until now. I have kept Kontakt up to date with Native Access; I keep all Kontakt instruments on an external drive.
I use Kontakt in practically every tune I write (using Pro Tools Studio). Over the last week or so I was working on video, but when I came back to my latest Pro Tools project which uses 2 instances of Kontakt, PT displayed a warning that Kontakt couldn't its instruments. Apparently, it had lost the paths to samples for a large number of instruments, throwing up a "Content Missing" dialog. The same thing happens in Kontakt standalone.
Usually, this problem is solved with the use Spotlight option, but after much experimentation I find I have to find each individual sample using Browse For Files. Once the instrument loads in, I do a Batch Resave but the next time I access it the same problem comes up.
Any help would be appreciated.