The dongle is documented here https://infocenter.nordicsemi.com/topic/ug_nrf52840_dongle/UG/nrf52840_Dongle/intro.html?cp=4_0_5 and there is also link to download schematics. Not sure if it helps but I know that some pins (more than just one) are tied to reset pin so the module can reset itself to bootloader (led is glowing) by setting pin. Maybe that's what happened to you and it is waiting in bootloader?
EDIT:
pins 25,23,21,19 are tied to reset => -DNEOPIXEL_LRCK_PIN=23 in board file is not a good idea with the dongle.
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The dongle is documented here https://infocenter.nordicsemi.com/topic/ug_nrf52840_dongle/UG/nrf52840_Dongle/intro.html?cp=4_0_5 and there is also link to download schematics. Not sure if it helps but I know that some pins (more than just one) are tied to reset pin so the module can reset itself to bootloader (led is glowing) by setting pin. Maybe that's what happened to you and it is waiting in bootloader?
EDIT:
pins 25,23,21,19 are tied to reset =>
-DNEOPIXEL_LRCK_PIN=23
in board file is not a good idea with the dongle.