So, to be clear, it sounds like you're working with purchased packages? If so, you may have to go to the
Savage Worlds forum as this one is for using the Authoring Kit to muck with the source code, which probably isn't available for purchased packages.
I can partially help, though. The reason why adding the items directly isn't working is that those data files are already loaded, whether you're using them or not. So you really are re-adding them.