What happens if a file updated for 1.2.1 is mod…

What if I modified a file that was updated in v1.2.1?
I was looking at the post by sunshine saying that these files are modified:
/xmlrpc.php – deleted
/wp-admin
admin-header.php
bookmarklet.php
categories.php
edit.php
options.php
post.php
wp-admin.css
wp-comments-post.php
functions-formating.php
version.php
wp-login.php
What happens if a file, more specifically wp-comments-post.php, was edited and is changed in the new version? What should I do? Just skip that file? Also, is this list accurate?
Thanks for any help!