I don't think it's 100% SK's fault, but they own a large part of it.
- It's quite normal you have to add the credit card info again when you make changes to a flight. I think it's by law that the airlines, web shops etc. are not allowed to add more charges to a credit card than agreed originally. So when you do changes to an order/itinerary, which means additional costs you have to provide the credit card details again. Not even if you have added your credit card to your EB profile are they allowed to use it without your specific approval.
- Flight reservations are normally only kept for 24 hours. If a ticket is not issues before the end of the 24 hours, the flight reservations are normally automatically canceled. Swiss are pretty hard on this. That said. I have had 2 cases where SK managed to hold the reservations for 3 days before saw they where waiting for my credit card details. But those bookings were done through e-mails to the Diamond customer service.
I can't recall whether you are EBD, but if you are, I would try writing to the diamond customer service e-mail, and explain the situation to them. They can sometimes make miracles.