Step One: Open Kontakt and select "Batch Re-Save" under the "Files" menu

Step Two: Hit yes when it asks if you really want to do this. You know what your doing right?

Step Three: Navigate to the kontakt library you want to improve the load time of. For this I'm using Adagio Violas. Make sure you select the entire folder, not just the instruments section and hit OK.

Step Four: Wait while it scans for missing files. Note that these files aren't actually missing, Kontakt is just missing the pathways to find them.

Step Four and a Half: If Kontakt dectects missing files (I got really unlucky here and none of my libraries had this issue, so no picture for this step)
Tick the box that says "Keep these settings for this session". After doing that use the manual browse on the right side and select the same folder you did for step three. I'll try to see if I get a picture up for this later.
Step Five: Wait while Kontakt re-saves the files. After this is done the window will disappear and you can go ahead and load your library.

Hope this helps!
EDIT: I've done this to all of my libraries now, and none came up with missing files. If you get that could you take a screenshot so I can add it to the guide?