update version without touching non-changes files

Is it not possible only update the changed files when updating to new version e.g 2.0.23 to 2.0.25?
Even there are no changes to files, but it updates all the files and so, if something changed, it will overwrite it, which is not necessary.
What is the best way to update the software without touching the files that are not necessary to update?
If I added something to the footer, I will be lost when update.

Unfortunately, that's not possible.