I *know* there has got to be a twist and I know I haven't been spoiled for it yet! Please enjoy some of my baseless speculation:
-the computer is cloning them and that why they reboot with only their backup memories and no recollection of the launch.
-they have rebelled against the computer before (hence the random blood inside the computer) and it wiped their memories
-his sister has been dead the whole time and the recordings are all fake or out date
-it's all a cusk experiment
-earth died and they are the last people and stuck there in space
-aliens are playing with their minds
-they are both androids!

I need to finish my book club book and then I am coming back to this!