Aggregated distributed energy resources (DER) units in the distribution networks are utilized to support flexibility services in modern grids. To ensure modern grid security, active and reactive flexibility operation must not increase the risk index of the integrated transmission-distribution networks. This paper assesses the impact of aggregated DER units on the distribution networks and proposes a bilevel optimization approach to mitigate the impact on the grid’s security. The bilevel optimization approach involves distribution network reconfiguration and flexibility quantity estimation. The probabilistic risk index and hosting capacity are included as security objectives in the reconfiguration problem formulation to minimize the total distribution network power loss. A decision tree classification approach is proposed to estimate the minimum flexibility MVA to achieve a desired voltage deviation reduction. The proposed approach was tested on IEEE 33- and 69-node distribution networks. Under a 100% increase in load at specific nodes, the proposed technique achieved a significant improvement of 16.67% in the voltage deviation of the worst nodes in both the IEEE 33- and 69-node test networks. The results show that the proposed bilevel technique optimally reconfigures the network and effectively estimates the flexibility support required to ensure the grid’s security during disturbances.