Due to Quartus® II bug, you might get SERDES missing port errors such as rx_signaldetect, tx_pipemargin, or tx_pipedeemph after you regenerate PCIe core in a different Quartus versions. This issue is documented in Table 20-2 in Megacore IP Library Release Notes and Errata (PDF).
Perform the following steps to get around this issue:
1. Remove <variant>_serdes.v under the project directory
2. Regenerate the PCIE core using MegaWizard or SOPC builder.