It appears that when a guild update happens, it is wiping out the character data for the characters that have been uploaded.

Strangely, I just now encountered this same behavior. My UU upload reported as "timed out" and when I checked my roster page, it had wiped out all the previously-uploaded character data. Checking the member log showed that I had removed and then re-added every member of the guild.

http://www.undeadfish.com/UFRoster/index.php

I'm at work now, but will be happy to provide data for troubleshooting when I get home.