Complex sentence: After 1806 the new German Kingdoms like Bavaria, Wuerttemberg etc. could name (e.g. "bavarian") "Freiherren", however these Freiherren were not "Freiherren of the holy Roman Empire", a.k.a. the "Reich".
Split into simpler sentences: After 1806 the new German Kingdoms like Bavaria, Wuerttemberg etc. could name (e.g. Bavarian) Freiherre. However these Freiherren were not Freiherren of the Holy Roman Empire, a.k.a. the "Reich".