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Virtual Credit Cards - HELP!

So we have a situation where a client had a virtual credit card for their booking.

Unfortunately, when they checked in, we charged them and they paid by debit card.

I am assuming that if we do not charge the virtual card then the customer will only have the 1 charge we took on the day using their debit card.  Is that right?  Would seem crazy to have to charge the virtual card and then refund it to the virtual card

Cant seem to find any clarity on it.  

All advice/answers greatly received