you can only transfer 1000 tracks 

I'm not sure I understand the issue...?

Sorry for the confusion

When I try to save my playlists to a FAT32 4TB drive after it's complete

it says only 1000 tracks per playlist can be saved. so what I end up having is a very slim down version of what's on all of my playlist.

If I use NTSF it can't be seen when I plug in the usb drive to play from it

only FAT32 works.

In earlier versions of rekordbox 6  I was able to do this........

so backing up both the collection and music files......is this my only option?

anyone?

It's a warning that certain devices cannot support playlists larger than 1000 songs. You can use larger playlists, but some devices won't read them.