Just delete one and update the other. The filmography is replaced on update anyway. (I don't recall exactly what the 'Merge Filmography' option does—I would just leave it off.)
I have a problem where I have a number of people who appear twice. The duplicates have the same name and each have movies associated. I don't want to remove the duplicates as they will no longer be associated with the movies.
Is it possible to select the duplicate people and merge them into a single entry or is there another way to merge them ?