I think I've seen something about the Mobipocket document initially being downloaded to the iLiad being named with the filename. Then when you open it the first time, the iLiad renames it to the "title" that shows up in the Mobipocket format. I'm guessing that's why it won't overwrite the old one, the names are different. I'm not sure how you can change that, but maybe it'll get you on the right track.
I also seem to recall it only doing that if you're syncing Mobipocket files to the Mobipocket folder on the iLiad. If you put them elsewhere I don't think it renames them.
I think you'd have to figure out if it's possible to change the filename during the sync (and make it the same as the title), or else have it put them somewhere other than in the mobipocket folder.
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