Another data point here. The same thing happened to me on ORD-MA 4410 (Republic), replaced with 9303 (Envoy). It threw my MR out of whack, too, as they rebooked me on non-stops. I called back and the supervisor was able to put the original routing back (That was originally a L segment and is now Y - which must have necessitated the rerouted booking originally).
I had just booked the ticket yesterday. Flight is for Nov 7.