When you refer to "Add Meta-Data", do you mean your plugin uses DocumentNoteUtilities to define the meta data type? The example we provide in the javadoc for that class demonstrates how to create the note type if it doesn't already exist. In your case I assume it already exists so it doesn't recreate the note type with the new fields within that note type. What you should do is programatically check if the fields on the existing note type are correct or not, and if they aren't just run the code that creates the note type again.
Alternatively, note type information is cached in your Geneious data location. You could switch to a new Geneious data location from preferences which will reset all your note types.