Thank you for your interest in the Intel Aero Platform.
We tried to duplicate your issue of going from Ubuntu back to Yocto, but we were not able to see the error. To narrow down the issue, we need to ask you a few questions: What image are you trying to flash back into the board? Also, what BIOS are you currently using?
Please note, a new image for the Aero (Version 1.6.1) has been released and can be downloaded from the following link: https://downloadcenter.intel.com/download/27399/Intel-Aero-Platform-for-UAVs-Installation-Files
Go ahead and try the new Aero image and let us know if that helps.
When flashing image v1.6.1, do you receive the same error message?
Have you tried using a different bootable USB flash drive?
Also, have you tried to reinstall Ubuntu? If yes, does it install properly?