Actually, this is technically how canon updates have always worked, it just happened behind the scenes before and was performed by interns. Characters can't just get shipped home and come back with new memories. Updated character are literally new people with the old memories inserted. The old character is incinerated/killed. I don't think the characters would react well if Val offered to kill them, clone a new copy of them and giving the new copy their old memories.

In this setting, there's really no other way to do it. Facility doesn't have any spooky jamjar forces that magically update characters. Even if Val did it behind the scenes, characters would still be dying, and it would probably cause an uproar IC (because if she can send them home why wasn't she doing that already, then the death thing probably would get revealed anyway).