In this paper, we propose a new set-partitioning model for the two-echelon vehicle routing problem with drones (2E-VRP-D), where partial routes corresponding to drone movements are enumerated using an efficient dynamic program. To solve the model we use an exact branch-cut-and-price algorithm, and a labelling algorithm for the pricing problem both based on state-of-the art literature. We also propose an adaptation of the wellknown rounded capacity cuts for this problem, as well as pre-processing methods to reduce the size of the problem. In addition, this paper presents an effective heuristic branch-cut-and-price, based on the exact branch-cut-and-price algorithm. Extensive computational experiments are presented, showing that the exact algorithm can solve all the instances from the literature on the 2E-VRP-D, and almost multiply by four the size of the clustered instances solved optimally. Sensitivity analysis is also conducted for the proposed improvements.