If you do not connect all RX channels in your LL 40-100GbE design, critical warnings inform you that some of these channels might be synthesized away by the Quartus Prime Fitter. Refer to the Quartus Prime Help topic at http://quartushelp.altera.com/current/index.htm#msgs/msgs/whssi_hssi_unused_rx_clock_workaround_not_enabled.htm.
To avoid the critical warning, you can add the assignment the Help topic specifies. You can also ignore the warning and allow the unconnected channels to be synthesized away.
This issue will be fixed in a future version of the Quartus Prime software.