A systematical examination of the chemical stability of cobalt metal nanomagnets with a graphene-like carbon coating is used to study the otherwise rather elusive formation of nanometer-sized physical defects in few layer graphene as a result of acid treatments. We therefore first exposed the core-shell nanomaterial to well-controlled solutions of altering acidity and temperature. The release of cobalt into these solutions over time offered a simple tool to monitor the progress of particle degradation. The results suggested that the oxidative damage of the graphene-like coatings was the rate-limiting step during particle degradation since only fully intact or entirely emptied carbon shells were found after the experiments. If ionic noble metal species were additionally present in the acidic solutions, the noble metal was found to reduce on the surface of specific, defective particles. The altered electrochemical gradients across the carbon shells were however not found to lead to a faster release of cobalt from the particles. The suggested mechanistic insight was further confirmed by the covalent chemical functionalization of the particle surface with chemically inert aryl species, which leads to an additional thickening of the shells. This leads to reduced cobalt release rates as well as slower noble metal reduction rates depending on the augmentation of the shell thickness.