Can you share more information like IP's, Quartus version and edition used?If possible share project.
So that we can study the scenario and provided you debug steps or provided solution.
The Quartus Prime software generates a warning message if your design contains unused transceiver channels. The warning message states that performance of unused channels may degrade over time if not properly preserved with the following Quartus Settings File (QSF) assignments - either global or pin specific:
set_global_assignment -name PRESERVE_UNUSED_XCVR_CHANNEL ON
Pin Specific Assignment
set_instance_assignment -name PRESERVE_UNUSED_XCVR_CHANNEL ON -to pin_name