Given a matrix polynomial W(x), matrix bi-orthogonal polynomials with respect to the sesquilinear formwhere µ(x) is a matrix of Borel measures supported in some infinite subset of the real line, are considered. Connection formulas between the sequences of matrix bi-orthogonal polynomials with respect to •, • W and matrix polynomials orthogonal with respect to µ(x) are presented. In particular, for the case of nonsingular leading coefficients of the perturbation matrix polynomial W(x) we present a generalization of the Christoffel formula constructed in terms of the Jordan chains of W(x). For perturbations with a singular leading coefficient several examples by Durán et al are revisited. Finally, we extend these results to the non-Abelian 2D Toda lattice hierarchy. CONTENTS 1991 Mathematics Subject Classification. 42C05,15A23. Key words and phrases. Matrix orthogonal polynomials, Block Jacobi matrices, Darboux-Christoffel transformation, Block Cholesky decomposition, Block LU decomposition, quasi-determinants, non-Abelian Toda hierarchy. GA thanks financial support from the Universidad Complutense de Madrid Program "Ayudas para Becas y Contratos Complutenses Predoctorales en España 2011".MM & FM thanks financial support from the Spanish "Ministerio de Economía y Competitividad" research project MTM2012-36732-C03-01, Ortogonalidad y aproximación; teoría y aplicaciones.