How are you doing the 'delete'?
If you need a refresh, you are doing it wrong
because Calibre knows what it does and all entries associated are cleaned up.
ONLY ever use Calibre to delete books IN Calibre. Never go beneath the skirts (into the Library folder) with the OS and do stuff there. That breaks stored linkages to the file.
IF you hav, the right click the Library Icon, run Maintenance:Check Library
And use that to fix the Missing books type errors. Extra books, is the one time you do use the OS to move those outside the Library folder, Then add them the normal way (if desired). <a cause for thes, is you used the OS to rename those book/folders and that also created the Missing error because it no longer knew where they were