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Why do you bother removing the books from Calibre after you just loaded them in to remove the DRM?
I just open them in Sigil from the Calibre library location if I need to make changes. If I'm doing really extensive changes, I might make a copy of the book first in the same directory (but you have that covered since you save the copies elsewhere).
And I don't see the point with using EPUBMetadataEditor, everything you mentioned can be changed either in Sigil or Calibre.
And no, that doesn't mess up the Calibre library database at all, the book title stays the same.
I've recently bought a series where each chapter has a nice graphic across the top of the page. Except they used a slightly different version of the same graphic for each chapter, and each one positioned slightly different by a few pixels. Once I made each chapter use the same one image and deleted 37 now unused, the size of the epub was cut in half from over 700kb to less than 350kb. I just don't get their thinking when they do something like that, it's just senseless bloat for no reason. So I'm pretty finicky like you about how the epubs should look and edit quite a few of them myself.
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