By default, Byonic will search for cleavages before a proline residue. However, unidentified cleavage sites before a proline do not count towards the missed cleavages limit. Similarly in Peptide workflows (Byologic), a digestion site followed by proline is not considered as a missed cleavage.
The behavior in the Chromatogram workflow (Byomap) is different. Here, the default is to ignore cleavages before proline. To change this behavior, the advanced command Assume Proline Cuts allows the counting of cleavages to include cuts at proline.