does it work?

certbot-nginx/certbot_nginx/parser.py

@@ -520,6 +520,7 @@ def _add_directives(block, directives, replace):
 
 
 REPEATABLE_DIRECTIVES = set(['server_name', 'listen', 'include'])
+COMMENT = [" ", "#", " managed by Certbot"]
 
 
 def _add_directive(block, directive, replace):
@@ -544,6 +545,7 @@ def _add_directive(block, directive, replace):
                 'expected directive for {0} in the Nginx '
                 'config but did not find it.'.format(directive[0]))
         block[location] = directive
+        block.insert(location + 1, COMMENT)
     else:
         # Append directive. Fail if the name is not a repeatable directive name,
         # and there is already a copy of that directive with a different value
@@ -553,6 +555,7 @@ def _add_directive(block, directive, replace):
         if location is None or (isinstance(directive_name, str) and
                                 directive_name in REPEATABLE_DIRECTIVES):
             block.append(directive)
+            block.append(COMMENT)
         elif block[location][1] != directive_value:
             raise errors.MisconfigurationError(
                 'tried to insert directive "{0}" but found '