Type Ill protein secretion systems (TTS systems), the subject of several recent reviews (Hueck, 1998; Galan and Collmer, 1999; Cheng and Schneewind, 2000; Staskawitz et al., 2000; Cornelius and Gijsegem, 2000; Plano et al., 2001) are found in many animal and plant pathogens and in at least one insect endosymbiont (Nguyen et al., 2000; Saltiel et al., 2001). With one exception, they are all proteobacteria, and that exception is Chlamydiaceae. Bacteria with TTS systems are usually host - cell associated at some time in their life histories, and the components of TTS systems are often virulence factors. In many of these systems, contact of the pathogen with host cells prompts delivery of bacterial proteins into the host-cell cytoplasm or cell membrane where they disrupt cellular functions to the benefit of the pathogen. Energy needed for delivery comes from ATP. Proteins of the secretion mechanism are conserved, but the secreted proteins tend to be unique to the bacterium secreting them. In proteobacteria, the TTS genes are clustered in the bacterial chromosome and have GC contents at variance with the rest of the genome, which suggests that they have been horizontally transferred. In the enterobacteria, the apparatus for secreting proteins by the TTS system is arranged in a supramolecular structure, the needle complex, which spans the inner and outer bacterial membranes, contains TTS proteins, and is thought to be the instrument of bacterial protein translocation into the host cell (Kubori et al., 1998. Blocker et al., 2001). Type Ill genes are homologous to those of the flagellar export apparatus from which they probably evolved.
You making a mistake in terminology, "Flagellar Export Apparatus" is not the same thing as a Flagellum. The FEA is a method for transporting proteins from the cytoplasm to the outside of the cell that can be used for an outside structure and in the case of type III it's also used for excretion. It was given the name "Flagellar" because that's where it was first discovered. Kind of the way Prostaglandins even though they are made throughout the body they were named after the prostate because that's were they were first discovered. So just like you can have Prostaglandins not from the prostate you can have a Flagellar Export Apparatus without a Flagellum.
Actually by bringing up the FEA you are strengtening the case for Evolution because not only was their previous functions/uses for the proteins in the Flagellum their was actually a precursor system for setting them up.