Due to a problem in Quartus® II Software version 13.1 and earlier, the recommendation for connecting unused GXB_RX and GXB_REFCLK pins for Stratix® V and Arria® V GZ devices is incorrect.
The pin connection guidelines document states, "Connect all unused GXB_RXp or GXB_REFCLKp pins directly to GND or VCCR_GXB or VCCT_GXB.".
The Quartus® II software .PIN file states,
"GXB_GND*: Unused GXB Receiver or dedicated reference clock pin. This pin must be connected to GXB_GND through a 10k Ohm resistor."
The Stratix® V and Arria® V GZ Pin Connections Guidelines documents are correct.
Connection of the GXB_RX and GXB_REFCLK pins to GND through 10k Ohm resistors will not cause any damage.
This problem is fixed starting with the Quartus® II version 14.0.