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.
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