You may run into problems yes... .

If you want to set your mind at rest, perhaps if the flights were booked less than 24 hours ago you could cancel and rebook, this time looking out for that box?

My experience of this:
I couldn't check-in once for a long haul flight and when I presented myself at the airport, they asked for the card used to make the booking. The card had been cancelled as I had closed the account, so I obviously didn't have it.

The person wanted to refund the amount (roughly £900) back to the cancelled card, and then make me pay again on a card I had with me (I assume/hope the same amount!). Since I didn't have any credit cards with me and I was 18 at the time, I explained the predicament and after ten minutes of typing away I was allowed to go. But I assume this was allowed because the card was in my name, the person travelling and I just didn't have it with me... .