You should only add the New book by dragging it (from KindleContent) to Calibre NOT by pointing Calibre to the Kindle content folder.

I view the Book in Kindle for PC, Then EXIT that ap. I then sort Kindle content folder by last modified date and NOTE the crazy file name. The I find the real book (AZW,Mobi...:Kindle Content type) that has the same base name
Find Duplicates Plugin might help you clean up the spillover.
Preferences:Adding Books: Adding Actions (tab): Set Automerge to your choice might help avoid dups.