I am in the like them tied together camp. It also seems to flow with the theme of a mega rich and famous developing Project: Timeless, where he was finding a way to live forever. So if, for example only, Damein Knight was running out of time in leonized bod, at least at the level he was used to. He could shoot money at some fun people at R&D to make his own reset button. The AI and Jr would be the prototypes of this black project, if I have correctly understood the gist of the last few posts. This gives them a really cool potential plotline. Soon the new total package Knight will rise and all the prototypes are a loose end that must gettaken care of. So you have a enemy, maybe hung out to dry, maybe borrowed time, maybe amnesia, maybe mysterious cyberware or cortex bomb and erased you could work into the origins.
From a GM perspective you can have two characters looking into their origins and slowly start a who's your daddy side hunt. They can run the lab where one was cloned, crack the server center where one was electrobirthed, do a snatch and grab of the scientist who ran the project, etc. In short your playing the Shadowrun version of Twins, ala DeVitto and Arnold. It has to be run. You just gotta do that.