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I can't repeat your problem, at least as I understand it.
Steps I took:
1) create a custom yes/no column called #mybool
2) put 'Yes' in some books (green check)
3) put 'No' in some books (red X)
4) leave some books as undefined (empty)
5) select the above books.
6) run bulk edit. I do not touch the box for #mybool, leaving it as 'undefined'
7) change some other metadata fields (I tried several)
8) Press OK
The booleans remain as they were. No changes.
What are you doing different from the above?
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