Kirk is, of course, the final authority on this, but from what I've figured out, this is not a problem if you have upgraded from TVEC3 or TVEC3.1 to TVEC 4.
What's happening is this... when you do a batch re-save Kontakt reads the NKI definition and updates the paths to the referenced sample files (wav, ncw, etc.) Now sometimes, when a developer updates an instrument they might skip certain samples, or even replace them, and in doing so they could also rename them. So that FF Middle C Pizz sample got a new name maybe?
If you keep the older (TVEC3 or 3.1)NKIs around when you do the batch re-save it will batch re-save them as well as the TVEC 4 NKIs. Not only does this take longer, it creates some confusion.
You want real confusion? There are at least two developers that leave unused samples in their packages. When you do a batch compress only the files that are referenced are compressed, so you end up with a bunch of files that don't get compressed. A real head-scratchin moment!
Now we'll wait for Kirk to correct me<G>!