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As you saw, calibre does not overwrite the.sdr folder.
However, if you delete a book with calibre, then re-add it, calibre will remove the .sdr folder with the book.
When deleting a book through the Kindle interface, if the book came from Amazon it will say "remove from device", and the .sdr folder will be deleted, since the contents are backed up on Amazon's servers. If you remove a sideloaded, non-Amazon book, it will say "Delete this book", ask for confirmation, and leave the .sdr folder behind.
If the book was modified, it is a moot point as the annotations will point to the wrong locations. If the book came from Amazon you can sync and the annotations will be migrated to the updated book by Amazon themselves.
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