Is it possible to upgrade (as from roomette to bedroom) when traveling on points? If so, how is that handled -- with the conductor, the 800 number, or direct with Guest Rewards?

If it could be done at all, I am confident that it would involve a call to Guest Rewards. Corrections from someone who knows are welcome.

It wouldn't surprise me if Guest Rewards would want to cancel your existing ticket and book a new ticket at current bucket. Since you imply your trip will have started, this might mean forfeiture of points already paid.

If you do accomplish an upgrade, please report the procedure and experience.

In the olden days, conductors were allowed to process on-board upgrades themselves. The upfare was always to the lowest fare bucket, so it was an economical way of snagging an upgrade if the advance-booking fare for the upgraded accommodation was a higher bucket.

Around the time that e-ticketing went into effect, rules changed and conductors were no longer able to process upgrades themselves. Customers can now upgrade only by calling Amtrak. The upfare will be the difference to whatever the accommodation is then selling for. For AGR tickets, the upfare would be the equivalent upfare in points (just the same as if you redeemed points for the upgraded accommodation). Apparently upfares can be done after the train departs, though I haven't seen any specific reports from anyone who has done it (and I haven't tried myself), so I don't know it's specifically handled, but I don't think you'll lose your previously redeemed points or incur any penalties or anything.

Basically, there is no longer any benefit to upgrading on-board (and conductors can't do it, so they'll instruct you to call anyway), so you might as well buy up to the better accommodation as early as possible to get the lowest possible fare on it.