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chaot - If you can extract the xhtml files and they have sensible names you maybe be able to reconstruct the broken epubs via an epub editor.
I suggest you 'validate' all your epubs with the
Quality Check plugin. Here's a few of the problems it can detect
Quote:
Find ePub formats that are invalid due to a missing container.xml file
Find ePub formats with invalid namespaces specified in the container or opf manifest
Find ePub formats that have non dc: namespace elements in the manifest
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I would move the broken epubs into a separate "Sort out later" physical library.
BR