Yes to both questions. Yes I would remove it from the deck and not use it. If you continue to use it, that will mean that card has a 50 % greater chance of coming up than any other card (as there would be two of them) in the deck, and that would prejudice your readings in favour of that card.
And yes, imho, it is a sign. The universe sends us signs in all kinds of ways. Take a good look at that card and at what it means to you. There is a message in there that the universe sent to you and wants you to think about.
And of all the cards to get a duplicate of: The World! It's like telling you that your Tarot readings will bring such deep beauty and meaning to you and help you create of your life the best of all worlds. Hey I know my cards have done that for me.
You can do whatever you want with the card, even frame it and hang it above your place where you read to remind yourself that you live in a universe where higher powers send us signs and communicate with us through Tarot cards.
Bar