JerryChang - thank you for the input.
We tried copying the files to the locations you mention and it still didn’t work. The problem – we think – is that we are trying to make a new board configuration alongside the standard devkit configuration. That is, we don’t want to copy over the standard tegra234-mb1-bct-pinmux-p3701-0000-a04.dtsi file. If we had copied the files to that location and overwritten the default files, it probably would work fine.
We finally got it to work without modifying the standard files, once we realized that p3701.conf.common defines functions that are then evaluated in flash.sh. Before, even when we wrote new PINMUX_CONFIG and new PMC_CONFIG variables in our configuration file, those variables were over-written by the process_chip_sku_version function call during the flash.sh execution.
To fix the problem, we further modified our board file to set variables and redefine the function. The new function does the same thing as the old function but doesn’t set PINMUX or PMC variables. We want to make sure that the PINMUX and PMC variables we set are the ones that get used. regardless of SKU or BOARD_FAB.