Save your clues to the cc database and use a unique puzzle id (eg the file name) as the citation - it’s then very easy to find specific entries and which puzzle they’re in via a database search.

Yes, I do this - I created a new database in database manager, and every new finished puzzle I choose Add puzzle clues to database, then tick the box that says Set Field Value, and add the puzzle name in the box. You can do this for each the old ones easily, too.