Somewhere along the line, the GPIO stuff in the devicetree went missing and the GPIOs stopped working.
/* Dummy driver to request setup for cape header pins */
cape_header: pinmux_dummy {
compatible = "gpio-leds";
pinctrl-names = "default";
pinctrl-0 = <
&P8_03_default_pin
&P8_04_default_pin
&P8_05_default_pin
&P8_06_default_pin
&P8_07_default_pin
&P8_08_default_pin
&P8_09_default_pin
&P8_10_default_pin
&P8_11_default_pin
&P8_12_default_pin
&P8_13_default_pin
&P8_14_default_pin
&P8_15_default_pin
&P8_16_default_pin
&P8_17_default_pin
&P8_18_default_pin
&P8_19_default_pin
&P8_20_default_pin
&P8_21_default_pin
&P8_22_default_pin
&P8_23_default_pin
&P8_24_default_pin
&P8_25_default_pin
&P8_26_default_pin
&P8_27_default_pin
&P8_28_default_pin
&P8_29_default_pin
&P8_30_default_pin
&P8_31_default_pin
&P8_32_default_pin
&P8_33_default_pin
&P8_34_default_pin
&P8_35_default_pin
&P8_36_default_pin
&P8_37_default_pin
&P8_38_default_pin
&P8_39_default_pin
&P8_40_default_pin
&P8_41_default_pin
&P8_42_default_pin
&P8_43_default_pin
&P8_44_default_pin
&P8_45_default_pin
&P8_46_default_pin
&P9_11_default_pin
&P9_12_default_pin
&P9_13_default_pin
&P9_14_default_pin
&P9_15_default_pin
&P9_16_default_pin
&P9_17_default_pin
&P9_18_default_pin
&P9_19_default_pin
&P9_20_default_pin
&P9_21_default_pin
&P9_22_default_pin
&P9_23_default_pin
&P9_24_default_pin
&P9_25_default_pin
&P9_26_default_pin
&P9_27_default_pin
&P9_28_default_pin
&P9_29_default_pin
&P9_30_default_pin
&P9_31_default_pin
&P9_33_default_pin
&P9_35_default_pin
&P9_36_default_pin
&P9_37_default_pin
&P9_38_default_pin
&P9_39_default_pin
&P9_40_default_pin
&P9_41_default_pin
&P9_42_default_pin
>;
};
The contents of the k3-j721e-beagleboneai64-bone-buses.dtsi file were different between the previous and current versions.
When I applied the above code to the dtsi and created the dtb file, the GPIOs worked fine.