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@petzi:
ZMI works perfectly 100% of the time for me.
I suspect that you just continued where you left off with invalid test data using an obsolete version of ZMI to add it to Calibre. Your "mess" should simply be deleted.
Read all of the ToolTips in both Tabs of ZMI.
Create a new Calibre Library for Zotero, and using the very latest ZMI version with the proper ZMI Options set, import all of your Zotero books and their metadata.
Use Auto-Step Mode with Auto-Select All CSV Files. Activate them in Options.
DaltonST
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