IIRC the ACES consist was bidirectional; it could operate in push-pull modes with either the diesel on one end or the electric on the other end. The train simply changed direction at Frankford Junction in Philadelphia, powering one engine down and starting up the other. One would think that while the train was in "push" mode, the dead engine up front served as the cab car.
Back to the Berkshire Flyer and Albany, this is brought to mind... for the time it would take to disconnect the engine, run it to a wye, run it around the rear of the train and then reconnect it, it might save some time to simply have a regular diesel ready to go in position to hook to the rear of the train while the first engine is being decoupled. Although there is no directional change, the Albany station crews should be familiar with positioning engines correctly as they do the dance of joining or splitting the sections of the Lake Shore Limited every day it runs.
Since I have no desire to ride this to Pittsfield and spend 43 hours 48 minutes at the downtown Pittsfield train station (or less if I cheat and take the Lake Shore Limited somewhere), I might just have to go to Albany and observe for sure how they handle this.