Lost Pages file in iCloud after update to Yosemite
The iCloud Drive directory is located within Mobile Documents. You can access iCloud Drive via Terminal with:
cd Library/Mobile\ Documents/
credit

Note that the Mobile Documents directory could not be found in Finder. You can get a list of sub-directories in Mobile Documents by typing
ls in Terminal. For example, the iCloud Drive directory for Pages.app is
cd Library/Mobile\ Documents/com~apple~pages
Try to find your documents in these directories. You may better keep offline to avoid iCloud syncing errors, if any, continue deleting your local files. If files are there, copy them out using cp.
If not, please try to log out your iCloud account in System Preference.app and re-log in. This enables OS X to re-fetch the iCloud files index and sync them again. However the chance it works is small, because your files are already missing on iCloud.com.
My guess is that some wrong operations delete all local iCloud Drive documents, and this change is synced to iCloud.com so all your online files are also deleted. The last solution would be to recover your files in iCloud Drive from a Time Machine backup.
Hope things go well!