Are you sure about that? How did you check it? Because the option ought to disappear in case there is no note with that value. So either you encountered a bug, or there are still notes with those property values.
You could use BBedit (Mac) or Notepad++ (Pc) or VScode (either) to do a search and replace across your vault for status: Done and replace it with status: done
All of those programs work across multiple files in one search operation.