Ok, here's another update
Rie142, CWatkinsNash - this might fix your issues, please give it a try. Thanks for asking about this - I really need people to report any issues with their specific environments as I'm more than happy to work on fixing them.
purple mink - this includes yet another check for invalid files - can you try it again?
seaquay - 0.7.45 looks like it fixed the issue with templates in columns, so try the latest plugin
CWatkinsNash - what can I say, but thanks for a thorough test and explanation. Its great to have the support of others!
The plugin was reading and using all the metadata.calibre data. But Calibre saves information on every book on the Kindle - even books no longer in Calibre. But it does flag which ones are in Calibre and which aren't. I was parsing all of them, until now. Version 1.3.3 should skip over any tags/columns in books that aren't in Calibre, which it should have done from the beginning.
There might be a couple bugs in Calibre that I'll follow up. If you delete a book, the metadata.calibre file is not updated to make the application_id null so the book appears to still be in Calibre if you read the file. And if you delete a book and reconnect the device, the application_id is correctly null, but the tag information, etc. is not cleared.