This paper presents an efficient algorithm for the simulation of multi-flexible-body systems undergoing discontinuous changes in model definition. The equations governing the dynamics of the transitions from a higher to a lower fidelity model and vice versa are formulated through imposing/removing certain constraints on/from the system. Furthermore, the issue of the nonuniqueness of the results associated with the transition from a lower to a higher fidelity model is dealt with as an optimization problem. This optimization problem is subjected to the satisfaction of the impulse-momentum equations. The divide and conquer algorithm (DCA) is applied to formulate the dynamics of the transition. The DCA formulation in its basic form is time optimal and results in linear and logarithmic complexity when implemented in serial and parallel, respectively. As such, it reduces the computational cost of formulating and solving the optimization problem in the transitions to the finer models. Necessary mathematics for the algorithm implementation is developed and a numerical example is given to validate the method.