Hi, Jana,
For production flash programming before it gets soldered onto a PCB, I suppose that you can develop a target board which integrates a socket which adapts to your package of LPC54606J512BD. After the flash is written, you can pop up the processor from the socket.
You can use the blhost tools or Flash magic tools to download code, in the condition, the processor must be in ISP mode.
Hope it can help you
BR
XiangJun Rong