yes, it could be the include reference to the old version.
Try removing that include reference so that only the include reference for the new webassist folder is present.
In many cases, I find that it is simpler to just recreate the email message using Universal Email 4. then t update it.
In the Universal wizard, you can select the option of creating a file for the email message this will allow you to edit the message directly in Dreaweaver without having to open the universal Email interface.