I had the same issue and tried this. It works --- but the books have to be converted twice!
The first bulk convert (unchecking the 'use saved conversion settings for individual books' box) changes the input format and other settings, but does not actually use those settings during the conversion.
When I bulk convert the same group of books a second time (now that they have picked up the correct input format and settings), the end result is what I wanted.
Seems like odd behavior. And twice the work.
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