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Originally Posted by WS64
First, Koreader now supports two calibre files. And these two files can have different custom fields in it, so at least I had to think of something.
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AFAIK Calibre saves the same custom columns in both files because you're only have one set of them. The ones in your library.
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Second, with the latest nightly (577, not sure if this is already in 568) Koreader writes the metadata in its own file which makes searching WAY faster (from the second search on), in my case it is more than factor 10 faster. If I have to consider custom fields here I again have to think how to make it still fast.
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You can try a 'Calibre Companion'-like approach.
Let the user choose (and define for you) the columns that s/he wants to copy over to the Koreader's metadata file.