In OS X Mavericks, you're going to be able to tag everything. If I was going to have to sync between different reading apps, I would TAG the specific books with the specific program I'd want to sync it with.
Then I would make SMART FOLDERS in my Documents folder of all the different eBook apps, and then tell them to only show the eBooks tagged with the app's tag name. Then I'd stick it in my Favorites on the sidebar. That way I can use whatever app I wanted and drag those books with ease into the different apps.
You would still be able to keep them in Calibre and make edits to the files within any app, it just needs to have the tags.
You could probably build an Automator script to make it sync into Dropbox, Box, SkyDrive, etc too with that setup. I know the code is out there.
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