We have had multiple times where the charges back to our Disney resort accounts were inaccurate and I would imagine it's the same with
DCL. You have to
fill in the credit card part in order to check in online and it does not give you options for linking different cards to different travelers in the same cabin/room.
The only way to check in early is to accept the charges for all in your room/cabin and sort it out at Guest Services later. Even after doing that we've had several mistakes made with family or friends in the same DVC villa. There have been several instances in threads here that have taught us to get a printout of our charges a few times a cruise/DVC stay and always the day before the last day. We've caught several mistakes. OP, I think you've done a good thing educating others what can happen - sorry it's such a large sum of money. I can't imagine they have that many refunds to process and it's really not a travel industry norm to take that long.