I'm not altogether clear on how you had things set up. Do you have auto-importing set up between iTunes & LW? That's where the songs are added to iTunes music library. Don't confuse this with the LW playlist that shows in iTunes.

Under iTunes File menu, there is an option to show duplicates. You can scan through that list to rid of duplicates. However can still be a long time process. iTunes compares the names only when showing duplicates, so checking their file size, bit rate, length etc. is wise.

To add the songs back to iTunes, go to your LW download folder. You can simply drag & drop the LW download folder onto iTunes Library icon at top right of the iTunes window (adding 9,000 songs at once will take a very long time.) However it's best to add them more slowly. Such as selecting first 50 - 200 or so & drag-drop them onto iTunes Library icon. Go through later and check for duplicates.

You will probably need to re-create playlists. Yes that could be a nuisance but see if the playlists are working after you add the songs back to iTunes first.