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Raman spectroscopy is a precious tool for the characterization of van der Waals materials, e.g. for the determination of the layer number in thin exfoliated flakes. For sensitive materials, however, this method can be dramatically invasive. In particular, the light intensity required to obtain a significant Raman signal is sufficient to immediately photo-oxidize few-layer thick metallic van der Waals materials. In this work we investigated the impact of the environment on Raman characterization of thin NbSe$_2$ crystals. We show that in ambient conditions the flake is locally oxidized even for very low illumination intensity. On the other hand, we observe no degradation if the Raman measurements are performed either in vacuum or on fully hBN-encapsulated samples. Interestingly, we find that covering samples deposited on the usual SiO$_2$ surface only from the top is not sufficient to prevent diffusion of oxygen underneath the layers., 7 pages, 4 figures. Johannes Holler and Lorenz Bauriedl contributed equally to this work