Point taken. I should refine my position: if a disruption for whatever reason means there's no trainset arriving at St. Paul from the west, so be it, there's no eastbound Empire Builder (EB) that day. But with the changes in engineers (and other crewmembers IIRC) as long-distance trains cross the country, I don't think EBs stuck in the Pacific Northwest or on the northern plains necessarily imply the absence of crews CHI-MSP.
So long as Amtrak can dig up at Chicago before the EB's westbound departure time an engine, a few coaches and a cafe of any car type, an engineer trained on the CHI-MSP route, a conductor, and a cafe attendant, I believe Amtrak should send them out as the EB on a CHI-MSP run, which can then be the next day's MSP-CHI train, and so forth until there are enough Superliners and crews in the right places to run proper EBs.
With the westbound EB leaving Chicago before the eastbound arrives, I realize that means two trainsets and two crews. (Possibly more crews if the eastbound EB leaves on time, the same engineer that arrives in MSP at 10pm not being able to leave MSP at 8am). But again, the engineer (and conductor and cafe attendant, IIRC) who brings the eastbound EB into Chicago isn't the one who came from Seattle or Portland. For the CHI-MSP crews (minus diner crews and sleeper attendants), it should be business as usual except for the train possibly consisting of Amfleets or Horizons.
