We provide a detailed history of the concepts of atomic number and isotopy before the discovery of protons and neutrons that draws attention to the role of evolving interplays of multiple aims and criteria in chemical and physical research. Focusing on research by Frederick Soddy and Ernest Rutherford, we show that, in the context of differentiating disciplinary projects, the adoption of a complex and shifting concept of elemental identity and the ordering role of the periodic table led to a relatively (...) coherent notion of atomic number. Subsequent attention to valency, still neglected in the secondary literature, and to nuclear charge led to a decoupling of the concepts of elemental identity and weight and allowed for a coherent concept of isotopy. This concept received motivation from empirical investigations on the decomposition series of radioelements and their unstable chemical identity. A new model of chemical order was the result of an ongoing collaboration between chemical and physical research projects with evolving aims and standards. After key concepts were considered resolved and their territories were clarified, chemistry and physics resumed autonomous projects, yet remained bound by newly accepted explanatory relations. It is an episode of scientific collaboration and partial integration without simple, wholesale gestalt switches or chemical revolutions. (shrink)