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@theducks, eschwartz: thanks for your responses!
OK.Then at least I didn't loose my metadata. It took my several days to organize my books.
@eschwartz: I used the Import/Export dialog...
My mistake was that I choose this option and I didn't have a backup. But I think is critical to show a message to the user that Calibre is about to overwrite the files in the configuration directory. I hope the developers do something about that.
My intention was to merge the two libraries from A and B on B and it' s still not entirely clear to me how to do it...
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