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OK, I see what you are doing.
The simplest solution for this is after you create your new ePub externally, select the old one in calibre, and drop the new one into the details pane of the display. calibre will then replace the existing ePub with this new one. Then you can use the Modify ePub plugin to update the metadata in the new ePub. You can also do this while editing the medatada. Drop the new file in the list of formats or use the add button to find it.
A few things I can think to add to what you are doing:
- You can add books to calibre without a format. Or delete the format after adding it in. This is the equivalent of your placeholder in iTunes but calibre handles it properly.
- Have you considered using Sigil to edit the original ePubs rather than extracting the text?
- I would probably use multiple calibre libraries for this process. One would hold the originals with any metadata cleanup. I would copy this entry to another calibre library (using calibre) and then clean the ePub. When satisfied with the cleaning, I would move them to a third permanent library. I occasionally do something like this, but I skip the first library and keep the original external to calibre until I am happy.
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