I don’t know but my guess is that they intend to do ancestor reconstruction of several different states in the evolution of the flagellum (the “re-engineering” part), and then from those inferred ancestral systems try to re-evolve descendant systems with new functions.
I see Matzke is already co-author with Baker on a paper using that approach to understand how ion-selectivity evolves (how the flagellum can evolve by mutations and selection to switch between sodium ions, or protons, to power movement):