EDIT: I was looking for this: https://support.native-instruments.com/hc/en-us/articles/210274985-How-to-Batch-re-save-a-KONTAKT-Library#:~:text=This%20means%20that%20the%20KONTAKT,KONTAKT%20Instruments%20within%20a%20Library !
In Native Access you can set the location for samples and pathes for the instruments (.nki).
As NA3 communicate with Kontakt the pathes are fixed inside.
Thanks Paule. Unfortunately these libraries don't show up in Native Access (I think there's a cost implication to doing that which some developers avoid?)
Anyway, I think I have a solution. I edited the post about 5 mins after posting - but you were so quick to respond that you won't have seen it ;)
No you can't, only for the libraries files, not the nkis.