Thanks, it worked!
The reason of my problem was not that I used an old version but that I used "Single-Step Mode" and stopped after the first button "… then Add Missing Books to Calibre".
With the different setting "Auto-Step Mode" and "Auto-Select All CSV Files" turned on there were different steps included and the "mess" in my database was cleaned up! It worked too in "Single-Step Mode" when I continued the process and pressed the buttons of the next group "Update Caliber Metadata Using Zotero Metadata" as well.
A wonderful plugin!
