Unable to target transceiver toolkit to HIP PCIe x2/4/8 instances

This is really confounding me. I have retargetted an altera example design (https://www.altera.com/content/dam/altera-www/global/en_us/others/support/refdesigns/ip/interface/pcie_svgx_avst_on_chip_mem_150.zip) to my own board and am trying to use Transceiver toolkit. The device is Stratix V GX. When I set PCIe core's number of lanes to more 1, I get following warning during assembler stage. After which the TTK is not able to recognize any channels.

Warning (15104): Quartus Prime software detected a bonding design. Reconfiguration is not supported for Bonded designs and MIF is not created for this design.

I saw another post about this error in this forum. That post indicates that paths may be missing or incorrect. But in my case, the funny things is that TTK is I do not get this warning and TTK console recognizes the channels if I only have one lane PCIe core.

BTW, I tried both Quartus Prime 15.1 and 16.0. Same problem.

What may be going on?

Thank you for the help.

Best regards,

Sanjay