I don’t see files missing from Skydrive in my Windows Phone Office Hub. However, if you do, Microsoft offers this fix.
How-to: Restore SkyDrive files missing from the Office Hub
The step-by-step process is described here in the Microsoft Answers Forum.
Issue opening Skydrive files and notebooks from Office Hub on WP7 and WP7 Mango
Addendum 2011.12.04: The fix also works the other way. I created a Word doc on my Windows Phone running Mango and was unable to sync it with SkyDrive. Reseting Office mobile on the device works. Be sure to email Office files on the phone before reseting. These files will disappear after the reset.