We extend and apply the Galois theory of linear differential equations equipped with the action of an endomorphism. The Galois groups in this Galois theory are difference algebraic groups and we use structure theorems for these groups to characterize the possible difference algebraic relations among solutions of linear differential equations. This yields tools to show that certain special functions are difference transcendent. One of our main results is a characterization of discrete integrability of linear differential equations with almost simple usual Galois group, based on a structure theorem for the Zariski dense difference algebraic subgroups of almost simple algebraic groups, which is a schematic version, in characteristic zero, of a result due to Z. Chatzidakis, E. Hrushovski and Y. Peterzil.