In-game reloading is notoriously bad. Carrying a dead body, saving and reloading will always make the body disappear, that is vanilla and unrelated to that collection.

As a usual rule, you should always quit the game and load only from the main menu. You can even break your save by loading in-game and saving repeatedly, as that will slowly add small errors here and there.

You can try loading that quicksave from the main menu but I'm not sure it will work. Best plan would be to load a save just before you killed him.