I'm fairly new to rail travel, and I've read this forum quite a bit, so I hope I don't sound ignorant here.
Will Amtrak cancel the entire ticket if a passenger doesn't show up for the first leg? and is the bus part even considered a "leg"? I know with the airlines, they will cancel a ticket if you don't travel all portions of it.
I was wondering if I missed the CS in San Jose, could I board in EMY?
Amtrak does not have an electronic ticketing/boarding system in place (yet, anyway)--everything must be manually submitted. That means that by the time they receive the tickets and process them and discover that one leg was missing, you've probably finished your entire trip. Additionally, the lack of electronic ticketing means that once you have that paper ticket in your hand, you are pretty much guaranteed boarding--even if Amtrak canceled your ticket, the conductor wouldn't know, since there's no real-time ticket checking. (I suppose if Amtrak really wanted to, they could issue a bulletin to your train's conductor to deny you boarding, but I'm not aware of any process for that.)
They can't really back-bill you, either, since it's possible to walk up to a ticket counter and buy a ticket with cash and no ID (or if they do ask for ID, I don't believe they copy your info down). Even if you buy the ticket online with your full address in your profile and give a credit card, they won't, since that would mean that credit card transactions are handled differently than cash/check/traveler's check transactions.
As far as boarding down-line, it's been said around here that virtually all conductors would not have a problem with this, especially if you tell them that you were trying to catch up to the train and would have missed the earlier stop. In fact, most conductors would probably be concerned that you overpaid for your ticket, since you paid for a stretch of track that you didn't use. I highly, highly doubt you'd be denied boarding or put off at the next stop for something like this!
The
only case where you might get in trouble for skipping a leg is on an AGR award ticket. There are some "loopholes" where you can get three zones of travel while only paying for two zones. The classic one is booking a trip from Slidell, Louisiana to Los Angeles (or anywhere else on the west coast). Slidell is one stop east of New Orleans on the Crescent and is in the Midwest zone (Atlanta is the break point for the midwest/east zones). However, AGR will not route you through New Orleans and on to Los Angeles on the Sunset Limited, since that would require an overnight in a hotel in New Orleans (which AGR does not want to pay for). So, instead, they send you all the way east to Washington, DC, then west to Chicago and on to Los Angeles from there. You can get a cross-country trip on the train for 2/3 the amount of points! However, if you live in WAS and want to get to LAX for less points, you might book SDL-LAX, routing you SDL-WAS-CHI-LAX, but then skip the first leg on the Crescent from SDL-WAS. If AGR finds out you did that, they may come back and debit an additional 10,000 points (or whatever the difference is) out of your AGR account, since your two-zone trip became a three-zone trip.
But for regular paid tickets, I don't think there is any danger in skipping a leg, especially if it would cost you more to reticket it!
Edit: but take note of Alan's special exception for sleepers above--I usually travel coach, so I always automatically assume the same whenever anyone posts a question here, and I forget about the different sleeper rules. If you are in a sleeper, first see how much it costs to reticket it. If that doesn't work, call the SJC station before the train departs and see if they can pass a message to the conductor notifying him that you are going to be boarding in EMY instead so he/she doesn't give your room away. That's still chancy but may help your case a bit. (Or, you can ask on the phone at the same time if the Amtrak ticket agent in SJC can do a manual override and keep your ticket price the same while still reticketing you from EMY.)