I can tell you what happened to me on this trip I am currently taking.....I booked a 2 zone redemption last September, NOL-CHI-LAX-SEA. AGR debited the 20,000 points from my account at that time.
On Tuesday, train 3 was 6 hours late arriving into LAX and so it missed the connection to train 14. Amtrak reservations rebooked me on a bus/train reroute to catch train 14 at Sacramento. Fine, and all worked well.
However, I just happened to notice my AGR account this morning was debited 46,013 points - but credited 24,955 - for a net loss of 21,058 points. These transactions occurred same day that Amtrak rebooked me on the alternate routing.
I called AGR and explained everything to the representative, who was very polite but not understanding the situation. She kept saying the net loss of my 21,058 points was correct. No matter how I tried to explain it, she couldn't understand that I already paid the 20,000 points last summer. And to take another 21,000+ points was a mistake.
She then consulted with a team lead at AGR and that person said the additional debit of 21,000 points was correct. I was trying to remain calm, and after a lot of back and forth I got the agent to agree with me that no transactions should have occurred on my account for this rebooking issue. It was an old AGR1 redemption and Amtrak adjusted the reservation to account for a missed connection.
To the agent's credit, she said she would escalate my concern to a manager. She did in fact call me back after a short time and said the AGR manager agrees with my math and that the points should be returned within a few days. I'll be sure to follow up, naturally.
One other strange item, the transaction to remove 21,058 points was for travel valid June 19, 2017. I told the agent Amtrak doesn't even book travel that far in advance - and she agreed - and said there are obviously some bugs with the AGR accounting system.
I wanted to share with situation in case you have a unique situation of an old AGR1 redemption but an automatic rebooking that triggers a point deduction from your account by mistake.