1. It would break connections with other trains.
2. It would have to be negotiated not just with BNSF (whom I wouldn't trust to actually live to up their agreement), CP and METRA.
I wouldn't trust CP either -- since Hunter Harrison is in charge -- and Metra might simply veto certain schedules, as they have a tight commuter schedule and any interference with that is a problem.
Also, there seems to be a *very* long lead time on significantly renegotiated schedules when multiple organizations are involved.
The Lake Shore Limited / Capitol Limited rescheduling seems to be taking a very long time -- which is perhaps unsurprising given that Amtrak must negotiate with multiple divisions of NS, multiple divisions of CSX, Metro-North, the MBTA, and possibly MARC, as well as Amtrak's own people at Washington, Chicago, Albany, Boston and NY, *and* there is trackwork & signal work going on at the Boston end, the Chicago end, between Pittsburgh and DC, between Albany and NY, and between Albany and "Hoffmans", *and* station alterations going on in multiple locations.
Probably any schedule which is proposed turns out to have some problem *somewhere* along the line, and it starts to seem advisable not to bother with changing it until some of the projects are completed.
Likewise, on the Empire Builder, it seems silly to change the schedule permanently until the mudslide work north of Seattle is done, until the station is moved in St. Paul, etc... and coming up with a *temporary* schedule which is agreeable to all parties may take so long that by the time it's agreed to, it's obsolete becuase the disruptions have relocated to a different area.
3. Most importantly, you would need a 6th trainset, and the equipment for that doesn't exist.
That is the key. I'm not sure where Amtrak found the temporary 6th trainset in 2012 (or was that 2011).