Just as Bluehost admitted, Justhost has also taken it upon themselves to a site wide script update of W3TC without your knowledge, and without a backup of your settings.
They offered me the option to opt-out of such future upgrades, which I agreed to, but I questioned why there were no communications sent to customers regarding such script upgrades being performed. I received no reply.
Here is the email from JustHost support:
Thank you for contacting support,
You're welcome to opt out of future upgrades, but yes, on Monday we pushed several upgrades of the W3 plugin to ensure the integrity of the servers to ensure that we can mitigate any future botnet attacks. Would you like us to opt you out of future upgrades?
Please feel free to contact us again if you have any further concerns.
[ redacted do not post other people's contact information ]