I did write back to The Blue Crown and got the following response (in part):
In making the decision to send the decks with the extra card, the thought was that any decks being opened can substitute the card easily, and the duplicate Queen could be thrown away or kept for magic tricks. Collectible decks, not being opened, would not need the extra card. You are right that for resale some months or years down the line, it can cause some difficulties.
Unfortunately, the vast majority of the decks were sold before the decks arrived to us, so we had no way of letting customers know prior to ordering. I will definitely make sure that a note gets added to the product page for any new orders.
We are also very surprised that USPC did not give us the option of a slight additional delay while they opened, added, and resealed, as that would not be a task that we could perform on our end.
Yes, any reprints will be easily distinguished from the first run so that people know which deck they have, even if it is still sealed.
It is possible that, depending on how many were/are printed/sold this deck may before more collectible, but we really won't know that until they start offering decks without the fix. Given that White Owls are supposed to be limited anyway, I would be surprised if they are ever corrected. Sounds like they will wait to sell out of existing stock prior to reprinting with the correction.
Poorly handled at the start but they are being very nice in their emails and extremely quick about responses.