What's the difference between a Cannondale F29 Carbon 3 and a Cannondale F29 *Flash* Carbon 3?
They look like the same bike to me. Its just different shops listing them in different ways. 

As far as I can tell, the specifications are exactly the same, but those shops have listed the parts in different ways. eg one has listed both hubs together, the other has them separately. And one specifies what saddle it is, the other doesn't. Both shops are showing the same photo.

Checking the 2013 Cannondale website, it just lists the F29 CARBON 3, no mention of "Flash". It looks like Flash was a brand used for the 2012 range, but for 2013 it is has been abbreviated to just "F".