Just got a question about metadata and whether it is removed when you flatten a PDF.

Removing metadata is a more thorough process than just flattening a PDF

see the following link:

http://help.adobe.com/en_US/acrobat/X/pro/using/WS4E397D8A-B438-4b93-BB5F-E3161811C9C0.w.html

So the quick answer is no, flattening does not insure that the metadata is removed.