[How lucky is it that you ask the one AI that does the tutorial!]

Fortuna keeps track of what you've done with your play history. What planets You've visited, how many times you beat the game, all that stuff. When the universe dies, it means you can't keep that history anymore, aside from select rewards and achievements and items and species you've created and whatnot. What usually happens is me and Mors- I mean Clockwork rip a hole into the new universe and get rid of the duplicates.