Being rebooked wouldn't necessarily affect ACI (Automated Check in). They would still need to be checked out of their original flight. Usually that is done by a human. I'm not sure that's part of the VIPR system. I feel like if it were this would happen all the time.

I've had dozens of occasions where the system (VIPR?) has "protected" me on a later flight, but it's never dumped my original flight unless the agent unchecked me in (i.e. they closed the flight I was supposed to be on). I never accept the reroutes on the app for this reason. I'm assuming it would uncheck me in and check me in to later flight (but that would be a human initiated action).