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I know that SugarSync (a Dropbox competitor) has the ability to apply permissions when sharing folders between different users. I have seen mention in the User Guide about only allowing some users read access to the folders/files - but whether this would stop them working with Calibre I am not sure. Therefore, whether this would solve your problem I do not know, but it might be worth checking out. If it all works with Calibre it should give you the sort of transparent syncing you are looking for.
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