Every 4d N = 2 SCFT T corresponds to an associated VOA V(T ), which is in general non-rational with a more involved representation theory. Null states in V(T ) can give rise to non-trivial flavored modular differential equations, which must be satisfied by the refined/flavored character of all the V(T )-modules. Taking some A 1 theories T g,n of class-S as examples, we construct the flavored modular differential equations satisfied by the Schur index. We show that three types of surface defect indices give rise to common solutions to these differential equations, and therefore are sources of V(T )-module characters. These equations transform almost covariantly under modular transformations, ensuring the presence of logarithmic solutions which may correspond to characters of logarithmic modules.