Hi, Prasanna,
Regarding your question, as far as I know the LPC546xx only supports SWD mode for downloading/debugging code, the JTAG port is ONLY used for JTAG boundary scan function, in other words, you can not use JTAG port to download code and debugging.
I have seen that the SWD signals are multiplexed with ADC0 pins for LPC546xx, I think you can use a jumper to solve the issue, in development stage, you can connect the SWD pins to a connector, while you can use a jumper to connect the SWD pins to ADC analog source. After development phase, you can close the jump, in this way, the SWD pins are ADC pins.
Hope it can help you
BR
Xiangjun Rong