Starting from the Stratix® V and Arria® V devices, nPERST dual-purpose pins were added, one for each quadrant in which a PCIe® core exists - device dependent. This pin is used to bring the PCIe slot reset, PERST_N, into the device and connect to the cores pin_perst port.
Prior to Quartus® II software release 12.0, the connection of pin nPERST to pin_perst was not enforced. When you migrate your design to Quartus II software release 12.0 or newer, Quartus will issue an error when this connection is not in place.
It is recommended that nPERST be used in your design and connected to the appropriate PCIe HIP's pin_perst port.