Hi Travis,
that sounds really weird: flashing the eMMC, as we now do, effectively wipes off its content and replaces it with our image, so I can see no way this could have happened without reflashing the eMMC with one of the beagleboard.org's images. Maybe some of the old boards have been mixed up with the new ones at some point?
If you want to flash the eMMC of a board, just run /opt/Bela/bela_flash_emmc.sh
and wait till the LEDs go off, see here: https://github.com/BelaPlatform/Bela/wiki/Manage-your-SD-card#copying-the-sd-card-to-the-emmc