Alice's history didn't change because everyone was still calling Alice and Kate sisters. My first thought was post-Crisis the Kane girls were triplets with the third becoming Alice but I think Crisis is a misdirect. If something happened in Crisis, everyone else should know about it yet the previews make it seem like everyone is surprised by it. If she's a doppleganger from another Earth, she should be taken aback by the differences in Earth Prime but she seemed perfectly at ease.
I love that in a world that now contains metahumans, dopplegangers, aliens, magic and highly advanced holography no one can believe that someone could impersonate Jacob. But then they also refuse to believe the lone witness when she says her stepfather didn't kill her mother when logic says she be lying about him doing it, not the other way around.