Topological insulators combine insulating properties in the bulk with scattering-free transport along edges, supporting dissipationless unidirectional energy and information flow even in the presence of defects and disorder. The feasibility of engineering quantum Hamiltonians with photonic tools, combined with the availability of entangled photons, raises the intriguing possibility of employing topologically protected entangled states in optical quantum computing and information processing. However, while two-photon states built as a product of two topologically protected single-photon states inherit full protection from their singlephoton “parents”, a high degree of non-separability may lead to rapid deterioration of the two-photon states after propagation through disorder. In this work, we identify physical mechanisms which contribute to the vulnerability of entangled states in topological photonic lattices. Further, we show that in order to maximize entanglement without sacrificing topological protection, the joint spectral correlation map of two-photon states must fit inside a well-defined topological window of protection.