You can position the cursor in the file, perhaps before or after opening the replace window, and then click Find repeatedly and then Replace And Find Next as appropriate.

Unfortuately Mathematica and computers in general lack the "do what I mean" button that magically fixes exactly what we want done and nothing else.

I suppose, if you know how to use it, you can open up something like the vi/ex editor on the saved notebook file and tell it to replace all matching strings between line nnn and mmm. When manually editing a notebook outside of Mathematica you need to delete the cached information in the Mathematica file, you can find that section by scanning through the file, and then save the resulting file. Be sure you test this method on a test file before you accidentally destroy hours or years of work on your real file.