This paper proposes a comprehensive methodology to update dynamic models of flexible-link mechanisms (FLMs) modeled through ordinary differential equations. The aim is to correct mass, stiffness, and damping matrices of dynamic models, usually based on nominal and uncertain parameters, to accurately represent the main vibrational modes within the bandwidth of interest. Indeed, the availability of accurate models is a fundamental step for the synthesis of effective controllers, state observers, and optimized motion profiles, as those employed in modern control schemes. The method takes advantage of the system dynamic model formulated through finite elements and through the representation of the total motion as the sum of a large rigid-body motion and the elastic deformation. Model updating is not straightforward since the resulting model is nonlinear and its coordinates cannot be directly measured. Hence, the nonlinear model is linearized about an equilibrium point to compute the eigenstructure and to compare it with the results of experimental modal analysis. Once consistency between the model coordinates and the experimental data is obtained through a suitable transformation, model updating has been performed solving a constrained convex optimization problem. Constraints also include results from static tests. Some tools to improve the problem conditioning are also proposed in the formulation adopted, to handle large dimensional models and achieve reliable results. The method has been experimentally applied to a challenging system: a planar six-bar linkage manipulator. The results prove their capability to improve the model accuracy in terms of eigenfrequencies and mode shapes.