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I'd create several books entries, each containing the omnibus book, but changing the series/# for each of the individual stories, then each entry can have all it's correct metadata, then when you get the time, you can use the tweak-epub function to edit the epub to make it just that one book. (then proceed to next when you have time)
Having the whole omniubus in each entry then won't require you to search out the actual entry you have it in each time.
Have a tag of 'Omnibus-To-Edit' to quickly search out which ones need separating, then clear that tag when edited.
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