The Stratix® IV GX/T and Arria® II GX Transceiver Toolkits use a non-standard transceiver PHY which instantiates a Reconfiguration Controller as one of its sub-components.
Instantiation of two transceiver PHYs in a single transceiver block violates the device fitting rule that only one reconfiguration controller can be connected to a transceiver block and will result in a Quartus® II fitting error.
You can refer to the Stratix IV GX Handbook for further details on transceiver fitting rules.
To implement more than one transceiver channel in a transceiver block, you can increase the number of channels in the transceiver PHY.