When you say you have lost everything do you mean you have no live TV and you only have your saved recordings. As I understand that when you start the upgrade it reformats the hard drive so your saved recordings should have been deleted, also the box will have restarted at some point.
Yes, the V6 Tivo system, settings and all recordings are irretrievably wiped from the box during the 360 set up. You should have been informed of this in the confirmation email before you went ahead.
This process starts after you have received your new 360 remotes, then you clicked on Home>Apps>360Upgrade. The box is then wiped, and then the 360 firmware is downloaded permanently replacing the Tivo firmware. Took 10 mins for me.
All recordings and previous settings will be deleted.