The casein micelle (CM) have been described as a protein assembly held together by interactions between phosphoryl groups from the protein moieties, and several internal calcium phosphate nanoclusters (CCPs). While the presence of protein inhomogeneities at the small scale, sequestering the CCPs, has been widely accepted, the presence of medium scale inhomogeneities, the so-called "Hard" regions, and its relationship with the CCPs, has been object of debate. In the present work, solid state NMR and SAXS data have been combined to study the correlation between the removal of CCPs and the structural modification of the micelle. A << native >> sample and three different demineralized ones; 5% (DM-05), 10% (DM-10), and 25% (DM-25) of calcium in relation with the "native", have been analyzed. NMR data show that the reduction in the total amount of calcium and phosphorous ions (-5%, -10% and -25% respectively) in the samples is not always equivalent to the loss of CCPs as measured by the decrease of the amount of colloidal P-31 (-15 and -17% and -25% respectively) in the samples. NMR data also indicate, that demineralization induces the total depletion of some CCP while leaving the remaining cluster in a rather "native" like structure. SAXS data show a good correlation between the amount of P-31 loss measured by NMR and the decreases in intensity for the SAXS spectral features associated with the nanoclusters. Finally, SAXS data show the demineralization induces a decrease in the amount of the larger inhomogeneities in the micelle (the so called "Hard" regions). However, this decrease is not directly correlated to the decrease in the amount of CCPs (as measured by SAXS and NMR) indicating that these "Hard" regions may be, at least partially, maintained by a large protein-protein interaction network. The data and results are discussed and compared with different structural models of casein micelle.