The purpose of testing is to verify your assumptions. Even if you think you are sure of them
So, if Boeing learned something from ZA003 (which is in fact a nice way of saying they underestimated something in the design stage, and hit a snag), then it is only good project management to go sort out the issue at hand, and in the mean time have the remaining test work divided up over all available prototypes, for as far as that's possible.
When introducing new technology to such complex systems such as this aircraft, you are bound to hit some setbacks.
I don't think it's just Boeing that has these "problems". To any degree, they are symptomous to any high-tech project.