Mutually Orthogonal Cellular Automata (MOCA) are sets of bipermutive CA which can be used to construct pairwise orthogonal Latin squares. In this work, we consider the inversion problem of pairs of configurations in MOCA. In particular, we design an algorithm based on coupled de Bruijn graphs which solves this problem for generic MOCA, without assuming any linearity on the underlying bipermutive rules. Next, we analyze the computational complexity of this algorithm, remarking that it runs in exponential time with respect to the diameter of the CA rule, but that it can be straightforwardly parallelized to yield a linear time complexity. As a cryptographic application of this algorithm, we finally show how to design a $(2,n)$ threshold Secret Sharing Scheme (SSS) based on MOCA where any combination of two players can reconstruct the secret by applying our inversion algorithm.