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I'm recovering some of the .epub books by moving the good copy forward to the latest library. That seems to be holding up so far.
I do find scattered blog posts over the last few years where people did get zero size files in Calibre for one reason or another (or, mostly, no known reason I can find). So it may be either misreading one of the instructions and doing something I should know better not to do -- or some rare bug not understood.
Dunno.
Oh, and there's no case I've found where a file that lacked an .epub acquired an empty .epub file (or any .epub file) spontaneously, if that's what you asked above.
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