I assume you are talking about the theory of irreducible complexity. If that is the case, then if you take away any part of the bacterial flagellum, then what you are left with has no function. However, if you take away 40 specific parts, you are left with the Type-III secretory system, which is responsible for (among other things) bubonic plague, etc. This is not a flagellum, and is a relatively new discovery.
Not only that, but almost every other protien in the bacterial flagellum is strongly homologous to protiens that have other functions in the cell.
I thought you were a medical doctor? Don't you study biology?