I know this is probably centuries old inquiry, but I just encountered this problem and what i did was this:
I had a save of the moment AFTER the Eden Prime mission getting Javik, when Victus disappeared. I loaded a save BEFORE the mission and checked that he was still there before the mission. Then I loaded the first mentioned save (the one AFTER the mission), went to check, and he was there once again. Solved.
HOWEVER, this might not be necessary. Maybe you just need to reload the save AFTER the mission is completed (and maybe shut down the game and restart it) and the game will remember he's supposed to be there. I just had an irrational notion that I have to remind the game that he WAS there before by loading an earlier save.
Hope this helps someone, I'm playing it for the first time so I was spooked.