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Your case is similar to mine, except that I use mostly readers that support epub and PDF. Converting from PDF is unnecessary and not usually very successful.
I finally decided that I really didn't need auto-conversion, because Calibre can do it when I send the books to the device if I don't already have a format supported by the device, and I can read them on my computer in almost any format without conversion.
Another approach would be to use a tag or custom column to keep track of the books that you want to maintain in multiple formats, and use that to exclude those books from the search.
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