In my Kontakt 7, I noticed all my Native Instruments libraries have duplicate files. Is there any way to get rid of them?
Well, if you right click the preset and choose Show in Finder, it should show you where the duplicated folder is. I would suggest to delete the duplicate folder and then reset Kontakt's database:
Will this delete user favorites? If so, how to export those?
This would only delete the duplicate factory files.
The favorites are found here:
On Mac: Macintosh HD > Users > "Your User Name" > Library > Application Support > Native Instruments > Shared
On Windows: C:\Users\USERNAME\AppData\Local\Native Instruments\Shared