Haha, it went quicker than expected! I slightly remembered that there should be, somewhere on the computer, a backuped database from the times when there was no error message. So I copied it and replaced the present database on the device - including the zipped folder with the files "affiliate.conf", "KoboeReader.conf" and "version".
And voilą: After the processing done, I opened Calibre and made "check database" with the result "ok".
Thank you, David, once more!
P.S.: The settings remained as they had been, only in the books I had on the hard drive, I have to look where I had been.
May I utter a suggestion: Could the automatic storage of a corrupt database be suppressed? I was about to replace the present corrupt database by another that I had stored before at first.
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