Complex network information systems are usually responsible for realizing client requests of business level services. Often these services are critical for the company and it is very important to ensure that appropriate reconfiguration will be applied in case of system malfunction. Due to the complexity of systems, huge amount of dependencies and impacting factors, the analytical approach may be too limiting to evaluate the reconfiguration policy. The paper presents a method of analyzing new applicable configurations of information systems based on simulation. As a result, the reachability graph of configurations is constructed. Each transition in the graph defines the most adequate reconfiguration (compliant with user criteria) in case of a system failure.