This probably will not be the only time that I write about RF Tools, as it is one of the most used tools within my Revit arsenal. It's parameter transformer feature is its most versatile feature and is an ideal for problem-solving.
"Phantom" keynotes are keynotes that fill out the keynote schedule on a sheet, yet the hexagon does not display anywhere on a sheet. They can be this way for many reasons (change in view range, hidden object, placed near viewport edge, etc.). They tend to be not easily found through conventional methods. The example below shows that a keynote that was place on a sheet but no Key Value was assigned so the schedule adds a number but no text was added.
Since no Key Value was assigned to the keynote, it means that the keynote text value in the properties palette will also be empty. I would use that as my option for tracking down the keynote and deleting it.
Parameter transformer is able to gather information on all keynotes within the model. It does have options select current view or the entire project. I usually select Entire Project because the current view will eliminate the option to see any tags that can in be found in any parent/child related views.
On the Excel Tab, select Key Value, Key Text, and Workset and Export these values out to Excel, Key Value is the value you apply for each keynote in the properties. Keynote text is the text associated with the keynote, this is what shows up in a schedule, it is the value associated with the Key Value. Workset is the name of the view that the keynote was placed on and is the best place to start sorting down whatever keynote you are looking for. When you try sorting down the list based on workset, pay attention to not only the name of the view which is on the sheet but also the names for any views that are also the parent or dependent.
The "phantom" keynote will be whatever row on a specific view workset, and most likely in the Keynote Text column will be completely blank. So for that keynote, copy the associated Element ID found in column A and paste it into the Select by ID feature within Revit so that you can then delete it.
This exercise can help you identify and resolve this issue in a matter of minutes versus blindly searching and unhiding items/categories to find the element in question.