I was contacted by an Amtrak GR CSR. I told her about my experience and she agreed that since Amtrak had authorized all paying customers to get a refund on their Mar 31 fare, I shouldn't be docked my miles either. So she offered me that she can either try to work this with Amtrak to get my 3000 points or I can be offered a $250 travel voucher for future travel. I went with the voucher. Thanks AGR Insider who saw my post here and initiated this follow-up calls/messages to resolve this issue.