Uncanny Dodge and Losing Your Active Defense Bonus

Uncanny Dodge only prevents you from becoming flat-footed. Flat-footed is a specific condition, defined on page 211 of the rulebook. There are very few abilities, challenges or stunts in the game that make the target 'flat-footed' (most make you 'lose your active Defense bonus', which is also a consequence of being flat-footed, but is not the same as being flat-footed).

Commentary on the Above

The way I approach Uncanny Dodge is that it works when you aren't consciously aware of a specific danger.

So in the surprise round, or before you act in the first round, you get the advantage. If at any time later during that encounter (basically until you drop out of initiative) your enemy uses his abilities to deny you your Active Defense bonus (whether it be a feint, a vertical strike, create distraction etc) then UD is no help. Your conscious mind is in control, and it just got tricked.

So, if an invisible/hidden monster attacks you completely from surprise, you'd get UD: it's a surprise attack, and 'something' tips you off, making you dodge at the last moment. After that though, you're actively looking for the target, trying to seek them out. Your mind got other priorities, and that instinctive edge is lost (on the other hand, you can make attacks. Seems worth losing the effects of UD for :) )