I have had many "you have been rebooked" but always ignored them and just gotten on the flight if I can make it. Also very surprised if the TSA actually knew your BP was cancelled...How could that even work?

[added] OP, I get some CRAZY stuff on the Delta app when I have late connections, including my original flight disappearing, but never have had a problem if I just hand the GA the paper BP and get on the original flight.

Doesn't mitigate your point that this shouldn't happen without human intervention...but I don't think they actually cancel you off the original flight until you miss it, despite it looking that way.