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A little update.
The original author of the zip library I'm using is on it. But he think there might be a problem with the zip headers on the file sample I sent him.
I also made another test. If I open the original epub causing problem with Sigil and simply save a copy and replace the original by the copy then I don't have any problem with COPS / update_metadata anymore.
I also noticed that the rare epub I found causing problem contain the files ITunesMetadata.plist and ITunesArtwork meaning that they were tampered by Itunes.
So I have some clues but no real solution yet.
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