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I have never done it nor want to. I prefer ePub when possible.....
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I want to read only epub in my Touch, I really do. I find only Stanza that is capable to read epub and nice to use. (No iBooks for me, still on 3.12). I like Stanza's full customization and coverflow. But the way Stanza ignore some of css instruction in epub is really annoying. Also, it seems like there is no easy way to extract notes and annotation.
So here is what I do: I sideloaded converted mobi to kindle app folder. It reads all formatting and css instruction quite nicely. And then when I'm done reading, I just copy those file along with its mbp file extension which is containing annotation and notes back to my computer. That way, I have my annotation safely backed up.
Not perfect methods, but I prefer it that way.