Super-Earths with orbital periods <100 days are strikingly common. The migration model proposes that super-Earths grow and migrate inwards to close-in orbits where they are observed. As super-Earths migrate inwards they pile up at the disc inner edge forming chains of mean motion resonances. After gas disc dispersal, simulations show that super-Earth’s gravitational interactions can naturally break their resonant configuration leading to a late phase of giant impacts. The instability phase is key to match dynamical properties of observations. Yet, previous simulations have modeled these late collisions as perfect accretion events, ignoring fragmentation. In this work, we investigate the impact of imperfect accretion on the breaking the chain scenario. We performed N-body simulations starting from distributions of planetary embryos and modeling the effects of pebble accretion and migration in the gas disc. Our simulations also follow the long-term dynamical evolution of super-Earths after the gas disc dissipation. We compared the results of simulations where collisions are treated as perfect merging events with those where imperfect accretion and fragmentation are allowed. We concluded that the perfect accretion approximation for giant impacts is suitable to model the evolution of super-Earths in the breaking the chain scenario, from a dynamical point of view. Although fragmentation events are very common, only ~10% of the system mass is fragmented during a typical “late instability phase”. This limited total mass in fragments proved to be insufficient to alter qualitatively the final system dynamical configuration — e.g. promote strong dynamical friction or residual migration — compared to simulations where fragmentation is neglected.