I tried it and it works very well. I'm impressed.
The ebooks from Twilighted even have their author notes removed automatically, which I like. [just for the record, fanfics are for my wife (especially stuff from Twilighted) not myself.
My only gripe is that it doesn't create an inline Table of Contents.
I have a Kindle, and I need an inline Table of Contents (yes, I know Calibre can make one, but I prefer the TOC to be at the beginning rather than the end.)
Can you set it up to create one?