@They should have flown as scheduled
No they shouldn't...the flight test data would've been invalid cos they would, effectively, be flying a different airframe. Which isn't helpful for the FAA/JAA certification. So they would've had to have repeated the tests...which would have been even more demoralising for said Boeing employees, pushing to do a pointless test knowing full well they'd have had to repeat the test anyway.
Sounds like Boeing management had their project-planning caps on for a change. Airtime in a flying test bed is veeeeeeeery expensive, hence why they stuff the thing full of instrumentation and follow the 'do it right first time' approach, and try, as close as possible, to match the production aircraft.
Incidentally, at a presentation given to us as final year engineering students, shortly before the launch of the A380, the Airbus wonk claimed that "we don't build prototypes anymore".
Me: "So who are you going to sell the first aircraft off the line to, the one that's been stuffed with the aforementioned instrumentation?"
AW: "Oh, that's got too many holes and extra wires in it, we keep that, as a flying test bed, for testing future upgrades and the like"
Me: "So the difference between that and prototype is?"
Yes they do, but structural analysis (FEA, etc) will only tell you so much, especially as far as composites are concerned...hence why they test it 1:1 scale before they let the wetware take it for a spin...
It's worth bearing in mind that CAD stands for Computer AIDED Design - doesn't remove the need for the good ol' Mk1 Greymatter. Nowt more dangerous than a CAD-jockey just unthinkingly throwing stuff together in the virtual environment and expecting it to work IRL...
The one with a copy of "Basic Concepts of Engineering" in the pocket and the flame-proof lining.