I notice the project wizard generates a board.h with macros containing symbols that the config generators (pins) no longer define, the macros in question are LED_RED_INIT, LED_BLUE_INIT, LED_GREEN_INIT and the macros are the IOCON_PIO_* macros.
This is for an lpcxpresso55s69 board.
oh, it looks like the relevant defines might be in fsl_iocon.h, I did have a board.h at one point that I think used the IOCON_PIO defines, but I can't reproduce it anymore. Feel free to consider this resolved.
I'm using Version 11.3.1 Some photos are attached.
The first is from the pins configuration window, after enabling a new pin, and you can see that it's generated quite different code that for the pins that were enabled in the project template.
The second is board.h, and we can see the macro LED_RED_INIT refer to IOCON_DIGITAL_EN, which, while it's defined in this project because the project template had some pins enabled, if you disable all the pins, save, then enable some that macro will no longer be defined, since pinmux doesn't use it anymore with the new style.