Hello John,
it's hard to tell why it failed. I have an idea though, and suggest the same as the script:
Please try again, but if problems persist, please let us know.
One possible explanation for the error is that the running BIOS wrote to the flash after flashrom did. Alas, that's possible. The Protectli folks also seem to expect issues like this as they also mention the retrying on [1]:
"If the flash has failed DO NOT turn off or restart the Vault and run the script again from the instruction above."
Normally, there is no reason to retry because the flashing procedure is quite deterministic. Unless another program also writes to the flash :-/
If you try again and the issue persists, I would try to figure out if this "Flashli" made a backup. Writing that back might increase the chances that the device still boots, even if flashrom shows a verifi- cation error.
Hope that helps, Nico