Due to a problem in the Quartus® Prime Pro Edition Software version 24.2, when the RX adaptation mode is set to manual mode, the CDR LTR and LTD status signal might toggle when you apply a reset during user mode.
There is no workaround in the Quartus® Prime Pro Edition Software version 24.2 and earlier.
You need to reconfigure the device to overcome the problem and ensure the correct functionality of the GTS Transceiver.
This problem is fixed beginning with the Quartus® Prime Pro Edition software version 24.3.