With a Voyage, I would suggest converting to azw3/KF8. It is a better format.
As for the issue with the books being kept, one of my acquaintances who has multiple ereaders keeps ePub in their library and converts to other formats as needed. For their puposes, they enter 'formats:"=EPUB" and formats:"=AZW3"' (remove the 's) in the search bar to select all books where both ePub and azw3 formats exist and then use the Remove files of a specific format from selected books tool to remove the azw3 format files.
If you see all your books with the selected books highlighted, I would suggest going into Preferences => Searching and checking the Show a quick toggle button... checkbox. This will let you see a button next to the Search button to toggle between only showing selected books and highlighting selected books.
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