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That would require changes at too many levels of the calibre internal design. calibre is not really meant to manage documents you are actively working on. It's meant to manage large document collections. If you are actively working on a document you should work on it outside calibre, and put it into calibre once you're done.
A workaround I sometimes use for the epub-to-epub issue is to rename the master epub file to zip. calibre can convert a zip to an epub just fine.
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