The Project Notes Import template requires a "Notes import ID" field in order to identify a specific project note. (Using project import ID would just add a new note.) This field is not listed in Query -- could it be added to Query? These are the only options available in Query: Notes, Notes author, Notes date, Notes description, Notes title, Notes type.

For custom fields, the "custom field import ID" is an available field. So the same should be available in Query for Notes.