Adding transition effects to FLV files without re-encoding

I have several rather large FLV files that I want to make into a highlights vid. I'd like to smoothe the joins between the cropped pieces by, say, fading them in and out, but without having to re-encode the whole thing.

So far as I can tell, the various FLV cropping tools don't seem to offer the above. I have basic video knowledge such as how to put the video and audio files into a new container, but not a lot else.

What would you recommend?