Your narrative has few facts that are helpful, but I suspect that some of your issues are self-inflicted. Do this:
[1] Upgrade Calibre
Desktop (not portable) to 6.7.1. Not optional.
[2] Upgrade ZMI to the latest version for Calibre 6+, which is 1.0.76. Not optional.
[3] Upgrade Zotero
Desktop to 6.0.15. Zotero > Help > Check for updates. Not optional. ZMI requires the
desktop version, and not the cloud version or a network version. The Zotero Storage folder on your hard drive that was created by Zotero itself is what ZMI uses. Never the cloud version. Never a network location.
[4] Run Calibre for your ZMI Library. Library > Library Maintenance > Check Library. Say "yes" for everything, and fully repair your corrupted metadata and files.
[5] Make a careful manual backup of you metadata.db. Make another full backup of your Calibre Library, including the "books". There is a standard Calibre menu option for doing so.
[6] Run Calibre in full debug mode using " calibre-debug -g " so you can watch in real-time what happens within Calibre and ZMI while ZMI imports a Zotero CSV export file.
[7] Open the ZMI window.
[8] Read the ToolTips for ZMI by hovering your mouse over the various widgets and options. Save any changes, and ZMI will restart.
[9] Create a new Zotero CSV Export file for a
single Zotero item that you have previously assigned to a Collection for ease of comparing Zotero to Calibre using the "ZMI: Comparison" feature.
Do not make any manual changes to it in Calc/Excel. I suspect you have been making manual edits that have corrupted the CSV file. ZMI requires "double-quoted" delimiters, and a format of UTF-8. FYI, Calc has an "edit filters" option when you save a file: UTF-8, double-quoted delimiters.
[10] Exit from Zotero.
[11] While still in Calibre full debug mode, use the "Auto-Step" option for ZMI, while clicking the "Select single CSV export file" button. Select the CSV file created directly from Zotero in a previous step.
[12] Watch what happens both in ZMI, and then on the debug screen. Note that you can "select all" of the text in debug mode, copy it to the clipboard, and paste it into a .txt document to save it and upload it to this thread so I can see it.
[13] After [12], there is still much more to do. ZMI creates an identifier for "new" books, so click the button "show incomplete books". Calibre will then show in the search bar: identifiers:"=zmi:new" .
It also creates Calibre Identifiers for the Zotero ZKEY, ZKEYFILE, and ZCOLLECTION. The Identifier ZKEY is what is used to drive ZMI. If Calibre Identifier ZKEY is missing from the Calibre Metadata, then that item is "broken" and will not exist as far as ZMI is concerned.
[14] Select all shown books so you can continue updating their Zotero metadata in Calibre using ZMI.
[15] In the middle of the ZMI window for importing from Zotero, click the pushbuttons for "Update Calibre Metadata using Zotero Metadata".
When you get pop-up messages from ZMI, copy them to the clipboard and save them to a .txt file for future reference.
[16] Do NOT archive/delete the CSV file "yet".
[17] Click the "Restart ZMI" buttom at the bottom. After ZMI restarts, click the "ZMI: Comparison" Tab. Update the Zotero DB Directory to where it belongs on your hard drive (not network or the cloud). Click "Zotero Collection" to choose the Collection you want to compare. Hopefully, you assigned a Collection to the Zotero Item that you previously exported to a CSV file and imported to Calibre with ZMI.
[18] Click "Compare Zotero Collection Items to Calibre Books". Check your new Zotero item to see that it is now in Calibre. ZMI updates the Zotero Collection with the Identifier ZCOLLECTION whenever you click the "compare" pushbutton in the "ZMI: Comparison" Tab.
If that single test item works properly, continue doing the same thing.
If the debug log shows a failure during import of the CSV, that is the root cause of your issues. Post the CSV export file with the single Zotero item, the full debug log (saved to a .txt file), and the ZMI messages that you saved to another .txt file to this thread so I can peruse them.
DaltonST