@SweatyBrie
They didn't change the facts.
This concern was with reversing the memory erasing only focused on Arata and Chizuru because of the connection they have. Everybody else's memories of them are erased in order to keep the company on the downlow and to avoid suspicion when the younger versions of the subjects disappear.
Since Arata and Chizuru are both Relife subjects, both already aware of the program, there should be no problem with allowing them to both keep their memories. However, since this is the first time they've had two subjects during the same experiment, how to possibly reverse the memory erasing effect was scientifically unknown.
The mediacal professionals at Relife are only partially certain that the memory erasing is irreversible. Everything was experimental, so they aren't certain what would happen until the end of the experiment.