I'm having the exact same issue with my ODroid N2+, Armbian installed on SD card. System runs totally fine without USB HDD attached (or if attached after boot). But when rebooting it'll fail to start-up properly.
I'll look into compiling u-boot without the patch mentioned here. Any chance to remove this patch in the official builds? Citing the previous statement "it's not worth having it if normal Armbian operation is impacted" I think that's the case here, as I would consider connecting a USB HDD normal everyday operation. Thanks in advance.