@unboggling - in relation to your other thread/post you made copy to library will prevent the need for you to worry about keeping some sort of placeholder file for your empty books. That sounds a fudge you do because of save to disc (which copy to library is a better alternative for in that case).
The opf file should always be up to date as I understand it, at worst there will be a small lag between the opf file being updated from when you update in Calibre as it writes using a background task. I do not believe the book itself will get updated with metadata using Copy to Library though - so if you absolutely insist on that being "done" prior to the book reaching your final library then what you are doing is valid. However for anyone who only reads the books on their devices, the actual send to device/save to disk you do from your final library will take care of that anyways. Your other alternative is to use the Modify ePub plugin if you want to the book to already have the latest metadata at the time.
I always use Copy to Library myself (or to be specific - the Copy with Delete after Copy option), way less steps and effort than Save to Disk (which you must save, then delete, then switch, then add). But Calibre does offer so many ways to do some things, there are pros and cons with each sometimes.
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