Arria® II GX transceiver channel reconfiguration support is incomplete in the Quartus® II software version 9.0. The reconfiguration Memory Initialization File (.mif) required for channel reconfiguration is not generated by the Assembler. Refer to the Quartus II 9.0 Release Notes for more information and a workaround.
It will be necessary to re-generate and compile your design in a version of the Quartus II software when full support for transceiver channel reconfiguration is available.