In that case, you can include this in the main.c file:

...
        #if MICROPY_HW_ENABLE_USBDEV
        mp_usbd_init();
        #endif

        pyexec_frozen_module("app.py", false);
        goto soft_reset_exit;
...

This will skip the pyexec_file_if_exists("main.py") and the for (;;) {} REPL loop.

I assume your frozen code is called "app.py". If "app.py" is not working as expected, you will enter a "soft reset loop". In this case, reflashing the firmware with a non-modified "main.c" is the only way to rescue the board.

I don't know if this is in accordance with good practice, but you can try it.

I thought there would be a way of modifying something like MICROPY_HW_ENABLE_USBDEV or MICROPY_HW_USB_CDC in mpconfigboard.h. Is there not a way to do it that way?

mp_usbd_init does not seem to exist in my MicroPython source code. See error at end of this post. I also did a file search and could not find it in the source. See my version number in my 1st post.

I added this to main.c, it's between // VVVVV and // ^^^^^^^^^. Is this the right place?

    // Execute user scripts.
    int ret = pyexec_file_if_exists("boot.py");
    if (ret & PYEXEC_FORCED_EXIT) {
        goto soft_reset_exit;
    }

	// this is 1 of 2 parts to disable repl
	// VVVVVVVVVV
	#if MICROPY_HW_ENABLE_USBDEV
    mp_usbd_init();
    #endif

	// this is 2 of 2 parts to disable repl
    pyexec_frozen_module("app.py", false);
    goto soft_reset_exit;
	// ^^^^^^^^^^^^^^^^



    if (pyexec_mode_kind == PYEXEC_MODE_FRIENDLY_REPL) {
        ret = pyexec_file_if_exists("main.py");
        if (ret & PYEXEC_FORCED_EXIT) {
            goto soft_reset_exit;
        }
    }

mp_usbd_init does not seem to exist in my MicroPython source code.

/home/zacharyh/MicroPython/Build/micropython/ports/rp2/main.c: In function 'main':
/home/zacharyh/MicroPython/Build/micropython/ports/rp2/main.c:184:9: error: implicit declaration of function 'mp_usbd_init'; did you mean 'mp_uart_init'? [-Werror=implicit-function-declaration]
184 | mp_usbd_init();
| ^~~~~~~~~~~~
| mp_uart_init
cc1: all warnings being treated as errors
make[3]: *** [CMakeFiles/firmware.dir/build.make:2944: CMakeFiles/firmware.dir/main.c.obj] Error 1
make[2]: *** [CMakeFiles/Makefile2:1803: CMakeFiles/firmware.dir/all] Error 2
make[1]: *** [Makefile:84: all] Error 2
-e See https://github.com/micropython/micropython/wiki/Build-Troubleshooting
make: *** [Makefile:55: all] Error 1

Thanks very much for the help.

I tried this AFTER // Execute user scripts. and it seems to work fine. Not sure what the reasoning is to put it BEFORE.
Also, my app was "main.py" rather than "app.py".
Note that any prints in your code will still be displayed in Thonny.