Hi @SanthoshP
Just to clarify, PTA3 is not a JTAG or SWD pin, so its configuration should not interfere with the debugger connection.
Could you confirm whether LED D8 stays ON continuously? If it does, that indicates that the S32K311 MCU is stuck in a RESET state.
Also, when you connect the J-Link to the J40 (JTAG connector) and try to flash the MCU, do you get any error messages? If so, please share it.
Lastly, you mentioned that you are unable to program the MCU using either the onboard debugger or an external one, which suggests the problem might not be with the debugger itself. To help narrow things down, could you tell me more about the last project you successfully flashed to the MCU? If possible, please share the project.
BR, VaneB