How about placing a "Hard Copy Log" option under Tools in the ATO? Hard copy changes don't carry forward in updates but a Hard Copy Log to note those changes in the ATO would.
It would basically be a notepad where admins could store the notes about and code for hard copy changes. Maybe include the New Post CODE option from the forum to separate the code from the notes. Then they could easily be identified, cut, and pasted back in when an update is installed.