I think you've stumbled into a bug. I can reproduce this behaviour on FM10 to FM12.
When extracting content using the <$paratext> building block, FM ignores all formatting except for subscript, superscript and the font family properties. The superscript should be preserved and it is when either first applying the cross-ref or updating through the Edit > Update References... menu.
Something about the Book-level update is misbehaving. You don't have to go back to each cross-ref individually - just use the Edit > Update References... option in each file (a PITA, but at least it let's you get the final result).
I've reported this to the Adobe engineers.
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Thank you for your detailed response, Arnis .