Some of it's word-for-word identical, but the Collector's Edition is updated through to Nemesis (or is it the end of Enterprise?) wheras Fact Files end at Enterprise season one. The updates take the shape of minor rewordings, extra paragraphs, boxouts etc, as well as a few new pages (including stuff on the Scimitar and a Constellation-class cutaway, both of which are filled with conjecture as opposed to the canon-only fact file info).
The collector's edition's strength is the behind-the-scenes info. It's often fascinating.
I only got a few old second-hand collector's editions, but i don't think they cover as much as the fact files do - no Voyager, Enterprise or DS9, except in passing references.