  We investigated the structure-property relationship of Co$_2$MnSi Heusler
thin films upon the irradiation with He$^+$ ions. The variation of the crystal
structure with increasing ion fluence has been probed using nuclear magnetic
resonance (NMR) and transmission electron microscopy (TEM), and associated with
the corresponding changes of the magnetic behavior. A decrease of both the
structural order and the moment in saturation is observed. Specifically, we
detect a direct transition from a highly $L2_1$-ordered to a fully
$A2$-disordered structure type and quantify the evolution of the $A2$
structural contribution as a function of ion fluence. Complementary TEM
analysis reveals a spatially-resolved distribution of the $L2_1$ and $A2$
phases showing that the $A2$ disorder starts at the upper part of the films.
The structural degradation in turn leads to a decreasing magnetic moment in
saturation in response to the increasing fluence.
