How can I reset the Safari bookmarks in iCloud?
According to this detailed Apple Support Forum post the trick is to use Lion 10.7.2 and Safari 5.1.1 to force a flush of the Data.

Simplified steps:


Turn off bookmark sync on all devices except the Mac
Backup current bookmarks on Mac
Correct bookmarks on Safari on the Mac
Move the new bookmarks out of you Safari Library folder
Delete all bookmarks and wait for iCloud to update.
Move the new bookmarks folder back and wait for iCloud to update
Delete all bookmarks on iOS devices and re-enable sync.


It's laborious, but I am fairly certain Apple will release better tools for this process. Considering there normal rollout, they are probably handling these issues in phases. They introduced Photo Stream reset mid way in the Beta, so I am sure they will bring the rest through over time.