Sorry if you don't like the answer, but I would be very surprised to hear that anyone has had any leeway granted in a similar situation. You asked specifically if you could check-in on line but not take the flights and still get the miles. The answer to that is no. And I cannot imagine that you're going to get a change fee waived either. Perhaps if you had called close to the 24 hour mark you could make a case. Now it is highly unlikely.