In the case of UEFI, it’s possible (and even likely) that when the OS is installed, instead of storing the EFI binary at ESP:/EFI/BOOT/BOOTX64.EFI, it stores it at ESP:/EFI/OS-NAME/name.efi and adds an entry to the NVRAM with the location of the binary. If the eMMC gets removed, and the board gets turned back on, the bios will fail to locate this storage location and promptly remove it. Hence, it’s no longer able to find the OS.
I would test this theory, but my board is out of commission for some reason, so I can’t actually confirm this is indeed the case. If someone would like to test this (and isn’t sure exactly how), please let me know, and I’ll try to guide you through the exact process.