However, I think my proposed 2010 trip will be in segments. Part of the trip will be from AGR points and I probably will be booking at different times (exactly 11 months prior to departure for each segment).
Well the AGR portions are easy to cancel, no penalty there as long as you cancel before departure of the train you'll get all your points back. No 7 day rule there at all.
As for the paid portions, best advice is don't pick up the tickets. That helps tremendously in terms of avoiding penalties. And while I don't know just how you're plotting out what parts are paid and what parts are AGR, if you can make at least the second and possibly third leg AGR reservations, that would almost guarantee that your 4th and additional legs would be outside the 7 day window for cancellation.
Consider the following to understand what I'm saying:
1st leg: Silver Meteor to DC - paid - departing Aug 15
2nd leg: Capitol to Chicaago - AGR - departing Aug 16
3rd leg: Empire Builder to Portland - AGR - departing Aug 17
4th leg: Coast Starlight to LA - paid - departing Aug 19
Hurricane is scheduled to hit on the 14th of August and Amtrak cancels service on the 11th. Since the first train is cancelled by Amtrak no problem getting a refund. Next two legs are AGR so again no problem getting your points back. The 4th leg is still just outside the 7 day window if you call right away, so again if you haven't picked up the tickets, no problem getting a refund. Of course if the hurricane isn't scheduled to hit until the 16th, then this doesn't help. But still I think that you can see where I'm going with this. If at all possible use the points for the first legs of the trip, paying for the later legs as that increases the odds that you stay out of the 7 day window.
Even if you do fall within the 7 day window either because the cancellation of service happens too late or you just can't use your points that way, I still suspect that Amtrak would be understanding and waive the normal penalty since obviously you couldn't make the first connection with the Silver service out of service. But if even after speaking with a customer service supervisor you still can't get it waived, remember that you can still ask for a voucher instead of a refund. By asking for a voucher good towards a future trip, you get 100% of your money back and you can then use that voucher to replan your trip at a future date.
The voucher is good for one year and if for some reason you can't use it within a year, you can send it in prior to its expiration date and Amtrak will reissue you another voucher good for yet another year.
Thanks for the great advice.