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No. Sorry. I don't think so.
There might be some settings for your sync software to ignore some filetypes. That could perhaps be used to avoid having some specific book formats copied?
Also it may be dangerous to have other programs working on the calibre library while calibre is running. If something serious should happen to the library, the synced copy of the library may not be fully/immediately usable and a restore becomes unnecessarily difficult. I recommend that you shut down the sync software while you have calibre running.
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