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what is your reading device ?
it may be better for you to transfer your books manually rather than let calibre do it, then you can move only the coverless epubs from calibre library directly onto your device, using windows or whatever to copy the epub files from calibre library.
stick to copy, not move, & you should do no damage.
e.g. for each book. strip its cover with modify epub, then use open path in right window to show the file location. copy the epub file from there using your OS, and paste it either to a device folder or to some temp holding area ready for a manual copy when you connect the device
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