First things first. This is an amended version the first paragraph of my original post which should read:
I had noticed in the past that the normal count and regex count numbers didn't always match and decided to look into it.
Using the attached file, count the number of calibre9 and you will get of 120. The same with <em class="calibre9">. Using the regex terms below you will get a count and a replace count of 90.
Code:
<em class="calibre9">(.*)</em>
<span class="italic">\1</span>
Execute another replace using the same terms same and you wiil get a count of 18. At this point 108 changes have been made.
Go to line 102 of chapter 12 and you will find five instances of the terms in question. The first two have been changed the remaining three remain the same.
Regards - John