We report on the experimental and numerical observations of synchronisation and desynchronisation of bound states of multiple breathing solitons (breathing soliton molecules) in an ultrafast fibre laser. In the desynchronisation regime, although the breather molecules as wholes are not synchronised to the cavity, the individual breathers within a molecule are synchronised to each other with a delay (lag synchronisation). An intermediate regime between the synchronisation and desynchronisation phases is also observed, featuring self-modulation of the synchronised state. This regime may also occur in other systems displaying synchronisation. Breathing soliton molecules in a laser cavity open new avenues for the study of nonlinear synchronisation dynamics.