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It very much depends on whether the card supports multiple logical channels and multiple selectability. I actually haven't seen one in the wild so I'm guessing its a card limitation.
What's the card ATR?
If you are trying to connect to the card over both the NFC controller (card emulation) and the device interface from Android at the same time you will probably have a race condition. On the phones I have used, you can only have one active at time.