Flight substitution and reroute is accomplished based on frequently updated flow constrained areas and a flight substitution system to minimize the impact of severe weather on the NAS. Each flight is assigned a route, a FCA controlled time of arrival (FCA_CTA) slot, a controlled time of departure, and a destination controlled time of arrival, wherein the flights are sorted according to the FCA_CTA slot to pass sequentially through an FCA. When a flight is re-routed, the subsequent flight FCA_CTA is updated with the FCA_CTA slot made available by the preceding flight. If such an update is not feasible, then the subsequent flight FCA_CTA is updated according to a slot credit substitution give-away method. The benefits and costs for rerouting a flight out of an AFP are input to an optimization framework for providing the best flight time and flight reroute options.