Hello calibre-user,
when automatic adding books you can do auto-merge:
calibre Preferences > Adding books > Adding actions:
Auto-merge added books if they already exist: Overwrite existing duplicate formats.
calibre Preferences > Adding books > Automatic adding:
Check for duplicates when automatically adding files
If a file already exists in calibre and you create a new pdf output of the file in your automatic adding directory, then the file is overwritten.
Greetings, Maria