So, I just went through all this in updating my SYNC3 version. I used the USB to do the update and the system showed that it successfully completed. However, when I sent the XLM file to Ford it showed the following message:
"It appears there is an issue with the uploaded log file. Our team will review shortly and update your account to reflect the current version of SYNC in your vehicle. We recommend using Wi-Fi updates where available for your vehicle."
Of course that has been over a month ago and Ford continues to show the same message. I contacted them after seeing the message and was told the USB method is no longer recommended and I should do the Wi-Fi update. My garage doesn't have the best Wi-Fi coverage so I pulled around back and proceeded to do the update via Wi-Fi and the system indicated it was completed successfully. Anyway, that was my experience.
I then proceeded to update the Navigation Software using USB, I did the download method from Ford, which completed successfully.