I also faced same error but i fixed this by editing the def config files in the custom_manufacturer (it may depend on what you have named the board under which manufacturer) folder to reflect the paths as same as your custom board in CONFIG_ARCH_BOARD_CUSTOM_DIR variable.
There will be two defconfig files in the nuttx folder, you have to change it both as I stated above. One will be under nuttx-config/bootloader other will be under nuttx-config/nsh of your custom board directory.
Hope this clears up everything.
Regards.
DKR