Hi,
it smells like there is something initialized twice and is allowed to be only once.
You use Processor Expert setup and believe you made some adjustment.
Some registers are write once only. For example MODRR, CPMUCOP register which routes peripherals to pins. When you use normal mode (no BDM) the if it is set for the first time then it is not re-writable.
Moreover, you only describe it does not communicate. Have you tested the MCU is working and not still in the reset phase or in loop start-reset caused by COP setup...write once only?
Best regards,
Ladislav