It happens to me every time I do F&R.
Today I turned my computer on.
When it was booted up, I connected an external HD via USB.
I Loaded Sigil, opened the book I am working on.
Went to the last Chapter and split it at the end of the chapter.
Loaded Note Tab. I found the text file on the external HD and opened in Note Tab.
I did a Control A, then Control C.
Went to the new last chapter in Sigil, did a control V in book view. All there.
Changed over to code view. All good, except for <div>xxx</div> instead of <p>xxx</p>
So did a Find and Replace. Find all <div> and replace with <p>.
They all changed, then I clicked on the code page and all the <div>s came back.
I then did another Find and Replace, clicked on the code page and the changed stopped there.
I then did a F&R for </div> to </p>, and they all changed, clicked on the code page and they still stopped there.
I have found that once I have done the first F&R twice, it all works as expected.
If I add another chapter, and have to do a F&R again (as above), I have to do the first one twice to make them "stick".
Hope this makes sense.