where do program instructions and items of data move during the running of a simple file update program?

Answer 1

Well, you'll need to be more specific than that.

A file update can be done two ways: 1) by completely overwriting the existing one with a brand new one, or 2) by actually checking the bytes in old vs. new files, make comparisons, and develope a "difference script", so a "patcher" can use the difference script, plus the "difference" in content, to stitch together a new file.

Approach 2) is definitely more complicated, and slower, theoretically, but the patch file would be tiny compared to the whole program.

Without knowing the internals of that "simple file update program", I'm going to guess it uses method 2 or something similar, thus the internals will move around.