Well, to eliminate collections as an issue, you can rename the collections.json file (in the system directory on the Kindle - its a hidden directory so you may need to type it in the file manager text box on Windows, e.g. E:\system if E: is your Kindle's drive). Then restart the Kindle - Home, Menu, select Restart, Menu, select Restart.
Check that your documents are in the "documents" directory on the Kindle. You can also use the plugin's "Edit Collections" option to list all your books which will show you if the books are still accessible in the usual way.
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