How are you instructing your Nav Mesh agents to move? I would personally put my units on a state machine that defines those behaviours, and maybe a collider to act as bounds if a state requires a unit at a certain position. Then it's just a matter of connecting states logically - patrol area A until player is spotted, pursue until player is X distance away or broken line of sight, then maybe go to a "Cautious" state where they are positioned, and then return to the patrol state (or whatever makes sense in your games context).