In Warlord it was established that the alien had taken control of Kes when he died. The alien, for all intents and purposes, broke up with Neelix and not Kes. Yet even though nothing else was blamed for Kes the break up still stood. Did I miss something? Was there another explanation given as to why they had broken up despite Kes' body being used by an alien and not wanting Neelix to uncover the plot?