see my responses in bold.
So - you published the form to the library, then opened the form from the library, filled out and submitted the XML, and then when you try to open the XML again, you get this message? Yes
You may want to check the Relink view in your library (make sure it is in classic mode - not sure what version of SharePoint you are using- SharePoint 2013 version) and see if all the XML are linked to the manifest location, or if any are linked to the published location. Sorry, I don't know how or where to look for the manifest location and the published location.
You may also want to open InfoPath Filler and under the New menu, find your template and either remove it or update it (right click on the template). You mean open the form by selecting Design, then look for the New menu? I can't find it and don't how to remove or update it. see the screenshot.