You may not see your transceiver channels in the Intel Transceiver Toolkit when using the Intel® Quartus® Platform Designer if you have left your transceiver reconfiguration interface dangling inside your Intel® Quartus® Platform Designer system.
To work around this problem, you can export your transceiver PHY IP and Tx PLL IP outside your Intel® Quartus® Platform Designer system and tie the inputs to ‘0’. You must still supply a clock and reset signal to the reconfiguration interface.