When you physically remove a card from a deck, you can just do the same in the deckstats deck. Your collection will still have the card in it but now it is freed up. When you now build your new deck with - say - all cards new except for this one card you pulled from your other deck, you just finish it and then add the cards to your collection. On the page that pops up you can now remove the one card that is already in the collection by hand.
As far as I know there is no simpler solution. There is a button to only add cards that are not in your collection but I believe this does not know about your other "active" decks. Maybe this is a feature that one could add to the website.