When deleting a book with calibre's Device View, calibre deletes the ondevice metadata (current page, annotations, pagenumbers, etc.)
So... don't do that.
Instead, just
resend the book. Assuming the send-to-device filename template remains the same and none of the metadata fields have changed in calibre, calibre will overwrite the old file with the new file.
The Kindle will notice the file was changed and reload it with the new metadata.
Note: The Kindle doesn't always handle that well -- if the book is in a collection it will turn the book into a "ghost". Instead, you need to delete it (the old copy) from the Kindle, unplug and let the Kindle realize the book is gone, and then re-add the book with the updated metadata. Do NOT accidentally delete (or let calibre delete) the *.sdr/ folder!
I typically update my purchases with fixed metadata + plugboards
before adding them to collections, so I don't bother to delete them first.
It is only an issue if the book is currently in a collection (because the updated book leaves behind a stale entry in the collections table linked to the same ASIN but the old title).