I posted a question about how to cure file bloat a while back. I didn't get a response from anyone, so I've been tinkering on my own. I had a project that went from 80kb to 178kb for some unknown reason. I went into my project, and selected every frame in my timeline. I then right clicked my mouse button and chose, "copy frames."
Then, I opened up a new project and selected the first frame in my new timeline. I then right clicked and chose "past frames." Not only were all the frames pasted, each layer was named correctly.
Most importantly, when I exported the movie, the SWF was back down to 104kb.
If anyone else has had experience with file bloat, I'd love to hear from you.