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@enonod - The Save to Disk feature is not intended to be used as a means to take library backups. It is primarily provided to allow users to copy the format files into a different folder structure with different file naming rules. It is possible to reconstruct a library from those folders and files via Add Books, however this could result in metadata loss.
Calibre does not have a facility to backup and restore libraries, I suggest using the same process as is used for other data - documents, emails, images, music etc.
I do an incremental backup of all my data every day to an external drive and once a week to commercial FTP service. The daily backup rarely takes more than 5 minutes, mostly two or three, the weekly backup typically takes about an hour. I normally run the backup within a shutdown script.
BR
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