Hi,
Is it the first time you download application code after design?
-> I have tested this board multiple times before this problem arrived.
are you sure that the power supply pins are connected correctly? I suspect that the LPC54606 can not start-up because of hardware connection.
-> I have downloaded code using Flash magic and it is working fine.

-> I am able to send and receive data on UART terminal.
-> I am able to send and receive data on CAN channels.
That means my hardware setup is ok and it's working. I just can't debug my hardware with JTAG.