notepad++ - How to merge list of words (remove duplicates)?

I am editing a long list of unique words (one word per line) in one text file.

I used Notepad++ and TextFXTools to merge list of words, and worked OK. I would add new words at the bottom of the list and used FXTools to remove duplicates.
It worked until the list became big, a couple of million words. Notepad++ frequently crashes with lists this big.

I need a way to add new list of words to one big list, delete duplicates and keep only unique words. How can I accomplish this?