Two things from my recent trip to Boston:
We boarded in Baltimore northbound and the conductor scanned out tickets from the app, no problem. Then, after we left New York, the new conductor came by to scan tickets, and my ticket was gone from the app! No real problem, the conductor just looked up my name, and it was fine. Same thing happened on the southbound. I've never had my tickets on the app disappear before the train gets to my destination. I might start printing my tickets as a backup.
The day before we returned, I got an email from Amtrak saying something about "check in" for the Acela. I ignored it and had no problem boarding the Acela at South station and having my ticket scanned. When we go to New York, all of the people boarding were taking out their phones and taking pictures of their seat numbers on the overhead rack. I asked one of them who was sitting next to us about it, and he said that he had gotten an email from Amtrak describing this new "check-in" requirement. They seemed to be some problems getting it to work, and when the conductor came by, he said he didn't know anything about this, and just scanned everybody's tickets, except mine, .of course, because my ticket has disappeared from the app. Don't know what that was about. I'm taking another trip at the end of the month, so I'll see if they still have it.