Remember in the episodes "Coda" and "Before and After" after Janeway was supposedly killed Chakotay was indeed then the captain/leader. So maybe that set a precedent for if KM hadn't returned? It seems would kind of stand to reason the commander would have taken over if no more KJ again. I recall when that was going on w/ KM; I was a little nervous that my heroine Janeway would be gone. Well anyway, it didn't happen, heh.