One may wish to start the process in a clean environment - 'clean' being a new calibre file specifically for Amazon titles and for nothing else.
1) Create a new calibre file
2) download every kindle book you own (a tedious process, depending upon how many Kindle books you own.
3) Put them all in to calibre
4) Go to bed (depends upon the size of your library).
The question now remains what to do with those Kindle books that now reside in the Kindle Folder in the Documents area. After all, those same titles now exist in calibre - where you can play with them to your heart's content.