The key to adjusting a DOE is being able to make good quick decisions and leveraging the data that has already been collected - when possible. For instance, if it is the first time you have ever evaluated Package-on-Package assembly materials there may be some things that you had planned that need adjustment. I certainly wasn’t sure if my target settings would work when our Package-on-Package work began. Another thing that will help you become flexible with your testing is making sure you have some spare chips/components and substrates, just incase you need to explore another set of variables that were not obvious before.
It’s not the end of the world if problems occur while you’re testing materials, in fact things can turn out even better if you relax, re-evaluate the situation, and redesign your experiment accordingly.