If the EB (or any other train) is unable to complete the whole trip by train, they still need that trainset somewhere, so they will run the train as far as logical before they put the passengers on buses. This way, they can use the same trainset for the return trip, bussing the passengers to the train.

Another possibility that is sometimes done is reroute the train around the affected area. Say there is some problem in MN. They may route the train from SEA to CHI via a different route through MN, but miss MSP. They would provide transportation to anyone going to MSP, but if you're going to CHI, you would just stay on the train.

These decisions may be made enroute. Unless it's a long term delay (such as a rockslide or bridge out that closes a route for 1 week or 1 month), you may not know prior to your departure from SEA. If that was the case, Amtrak would try to notify you (usually), via phone, online, or the CS agents would have that info.

I really don't know what would happen if you "jump train". You contracted to be transported from SEA to CHI. Amtrak is providing transportation from SEA to CHI. (True some is by bus.) But look at it this way, you fly from JFK-LAX, but the airport is closed, so they divert to SNA or ONT and bus you to LAX. However, you do not want to go by bus, so you leave at SNA or ONT. Should UA or AA charge you more since the fare from JFK-SNA or JFK-ONT may be more than JFK-LAX?