The MBTA doesn't have any official statement about this, but I wouldn't recommend doing it.
The CharlieCard is a contactless smart card, and it activates when you place it close to a reader. If you place two cards next to the reader at the same time, it's essentially random as to which one will actually be read and used. It is even possible for both of them to be recognized. Worse, if you have contactless credit or debit cards, those might also be read. Any of these will confuse the fare gate.
Since one of your two cards is empty, if that is the card the reader sees, then the fare gate simply won't open. If it sees both cards, the fare gate might do something silly like immediately open and close again. If you're feeling adventurous, you could try it out, but you could possibly lose money.
London's Oyster card is very similar, and Transport for London go out of their way to warn people against card clash, where multiple cards are read by the system at the same time. Since contactless credit/debit cards can be used directly to pay in that system, it's a much bigger issue there than in the US, where contactless credit/debit cards are uncommon (now, but in a couple of years everyone will have them).
As in London, in Boston I would recommend you always take out the CharlieCard you intend to use, and touch only it to the fare gate.