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As we explained earlier, Sigil will not create/write an epub without a container.xml file so something very strange is happening. My guess is some software is either playing around with the epub after Sigil creates it, or some anti-virus software is interfering with Sigil creating it. Its that or you or something is directly looking at the files and manipulating them inside Sigil's temp disk space, which is a very bad idea.
For example, if you are on a Mac and leave your machine on over 24hrs (say over a weekend) and don't close Sigil, the Mac OS itself will remove files from its temp for no valid reason, that can cause this problem. That is why we allow users to set Sigil's temp directory if need be.
So next time you get an epub that Sigil has supposedly created without a container.xml check its modification date and time to see when it was last manipulated.
If you are on a Mac or Linux box, please try running the following command on that epub and paste its output here.
unzip -t PATHTOYOURPROBLEMEPUB
That will show us modification times of the contents and test the zip (epub) for errors.
Please let us know what you see.
Kevin
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