MCU X works fine.

Then one day MCU X replaced with MCU Y. And MCU Y does not work.

Did you cross check to see, that if you plug back MCU X, it works still ?

I can see you grinning at this childish suggestion.

Assuming that you are using a 40 pin dip package, the effort of plugging and unplugging can cause hair line cracks in PCB traces and similiar faults if due care is not taken and the pcb is of poor quality. Have faced similar situations in the field.

Raghu