Impurity doping using Zn atoms was largely studied in cuprates because this process substantially reduces the superconducting critical temperature Tc without any effect on the pseudogap onset T*. Earlier theories missed the recently established ubiquitous presence of incommensurate charge modulations in these materials. The charge order is a consequence of a phase separation transition which we describe by a continuity equation of the local free energy density. The Zn atoms generate a local magnetic moment, freezing their neighbors' spins, slowing down the electronic segregation process. Then the Zn-doped properties are that of a granular superconductor whose size of the charge order modulations are dictated by the degree of phase separation.