As I said, in theory you should end up with no duplicates... Anything added since will appear as "new". It will be as if your city library lost its catalog and found a copy it had from 1995. There will be things on the shelves that are not in the list, and there will be things in the list that are no longer on the shelves, or are maybe on the shelves but have been reclassified and will appear on the list in the old entry format and if you refer to them using that you won't be looking in the right place (a broken link = !).
turingtest2 article: Make a split library portable - https://discussions.apple.com/docs/DOC-7392
You need to be very literal when reading computer things. The instructions for preferences have to do with "media" which many people misread as "library". Changing preferences tells iTunes where to start storing the media portion of the library from that point on, and optionally lets you relocate where old media are located, but media are only part of a library. I don't know how the other things ended up on the external but as you said you may have put them there yourself.
Here is how one normally relocates a library:
Moving a library: Quick answer if you use iTunes' default preferences settings: Copy the entire iTunes folder (and in doing so all its sub-folders and files) intact to the other drive, hold down the option/alt key while starting iTunes, and when requested to select a library select the iTunes Library.itl file in the copied folder.
When this is to a new computer put the copied iTunes folder in the default location of Macintosh HD > Users > *User Name* > Music (or Home > Music) then you don't even need to start with the option key held down, iTunes will automatically look for it there. (Make sure there isn't anything already in the iTunes folder there that you want to keep since you will be replacing it with the one you are moving.) Remember to authorize the computer in iTunes to your Apple ID if you use this to sync to Apple mobile devices or play DRM protected media (e.g., movies).
Certain items used in iTunes related activities are not stored in the iTunes library folder but in special folders. If you are moving a library to a different computer you may wish to copy these too:
- Apple Music cache files: http://dougscripts.com/itunes/2015/09/new-flush-apple-music-cache-files/
- iOS device backups, various preferences files: https://discussions.apple.com/thread/3285925
