Hi,
The contents you are changing are in the header & footer section of that particular order page so, you can just include the header & footer files in the exclude list on the autoupgrade page in "List of files/folders to exclude" and save it.
Exclude these files:
templates/orderpages/dedicated/cart_header.tpl
templates/orderpages/dedicated/cart_footer.tpl
Hope that helps you.
Thanks.