I have just uploaded a course with a small correction in one of the resource nodes in my manifest XML however I get a parse error (I have checked every single file by copy/paste from the XML to a browser and all items exist) stating that I am using an identifierref for something that does not exist.

Identifieref is an optional element used to refer to a resource used in the manifest.  If you use that element, but do not have a resource that is named the same, this parser warning will come up.  To fix it, either change the name of the identiferref or the resource so that they match.