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The warning message is left over from debugging - it can be ignored. I'll post an update that removes it - thanks for mentioning it.
I'm puzzled as to why restarting calibre has any effect.
If you have wiped your Kindle just recently and are able to test I'd appreciate you doing this again and saving some information.
Are you starting calibre first then plugging in the Kindle or plugging in the Kindle and then starting calibre (it shouldn't matter, but useful to know).
1. Remove your books/wipe completely like you did before
2. Send a the books you sent before to the device
3. Check your plugin's Customizations are set to create from tags (assuming that's what you are using) - if you didn't do this before mention this
3. Run Create collections
4. Click on Show Details to show the report - can you post it here - see if it looks ok
5. Can you then get and post your Kindle's collections.json file here? (Go to your Kindle's entry on My Computer in your file manager. At the top of the screen where it shows "Kindle" type in the box and add "system" without the quotes (to get something like "E:\system") then you should see the collections.json file
6. Restart your Kindle (eject the device, disconnect, use Home-Menu-Settings-Menu-Restart)
7. Are the collections there with the books you expect/matching what the report showed?
I'm wondering if the plugin is just reporting collections that are Kindle only - and since you wiped your books, those collections might have 0 books in them now, especially if you didn't actually setup Customizations. The report should make this clearer - but restarting calibre shouldn't affect this at all.
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