Ouch.  You're right.  I'll have to think that through some more before 
implementing anything.  
We actually have this problem already at the per-word level, but it's far 
less pronounced than with a sentence-level replacement.  
Any time we replace *anything* (from the find or spell dialogs) we can 
potentially lose interior character-level formatting.  However, people are 
far less likely to have inter-word formatting changes, so they're unlikely 
to notice that we nuke them.  
But having the same behavior in a trivial sentence-level replacement is 
bound to be more noticeable.  At minimum, we should localize the edit 
operations, which would help, but that's not a real solution. 
As I said, this needs more thought.
Paul