When updating an issue via email with the following tag at the end:

   [messages=+25;files=+10]

the change only took effect if there was no message created or file
added. Otherwise setting messages/files on the subject line is
ignored.

The key is not to trigger/run this code (from create_msg, but similar
in create_file):
 
             if self.nodeid:
                 # add the message to the node's list
                 messages = self.cl.get(self.nodeid, 'messages') # **
                 messages.append(message_id)
                 self.props['messages'] = messages
 
It looks like this code gets the message list from the database and
discards the pending changes. So the modified version of the message
field, created by parsing the subject properties, is discarded.