Hello Andrew:
Kai Liu is correct, you can use the OpenSDA on FRDM board to program your custom board. You need to populate the J11 header, and take the signals from there. You will use the Serial Wire Debug signals (SDIO, CLK) coming from the K20 OpenSDA.
But then effectively both MCUs would be in parallel, so to avoid collision cut the trace under J18 in the KL46 Freedom board.
Please be aware that with this you should be able to program the MCU on your custom board, but not to debug. For your reference you may want to check the next tutorials by colleague Erich Styger:
Using the Freedom Board as SWD Programmer | MCU on Eclipse
Debug External Processors with USBDM and Freedom Board | MCU on Eclipse
Regards!,
Jorge Gonzalez
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