In this paper, we analyze the properties of a complex network of predator-prey systems, modeling the ecological dynamics of interacting species living in a fragmented environment. We consider non-identical instances of a Lotka-Volterra model with Holling type II functional response, which undergoes a Hopf bifurcation, and focus on the possible synchronization of distinct local behaviours. We prove an original result for the near-synchronization of non-identical systems, which shows how to and to what extent an extinction dynamic can be driven to a persistence equilibrium. Our theoretical statements are illustrated by appropriate numerical simulations.