[Karellen]

Yes, I have found that you need to Beautify the book first to ensure all search results are captured.

I have also found that those that are missed are due to some instances using the No-Break space instead of a standard Space. So I also run a regex to remove those. Usually they are an additional space that is not needed, so I clear them out. It really had me pulling my hair out in my early editing days.

I have also found that when I untick "Wrap" it works as expected on a single file in the Editor, but when using All Files, the unticked Wrap setting is ignored and it wraps around to the start of the book and replaces unwanted instances and I end up with, as an example, <em><em>some word</em></em> which means an additional S&R to clear that out.