Short range correlated (SRC) nucleon-nucleon pairs in nuclei are typically studied using measurements of electron-induced hard nucleon-knockout reactions (e.g. $(e,ep)$ and $(e,epN)$), where the kinematics of the knocked-out nucleons are used to infer their initial state prior to the interaction. The validity of this inference relies on our understanding of the scattering reaction, most importantly how rescattering of the detected nucleons (final state interactions or FSI) distort their kinematical distributions. Recent SRC measurements on medium to heavy nuclei have been performed at high-$x_B$ (i.e., anti-parallel kinematics) where calculations of light nuclei indicate that such distortion effects are small. Here we study the impact of FSI on recent $^{12}$C$(e,ep)$ and $^{12}$C$(e,epp)$ measurements using a transport approach. We find that while FSI can significantly distort the measured kinematical distributions of SRC breakup events, selecting high-$x_B$ anti-parallel events strongly suppresses such distortions. In addition, including the effects of FSI improves the agreement between Generalized Contact Formalism-based calculations and data and can help identify those observables that have minimal sensitivity to FSI effects. This result helps confirm the interpretation of experimental data in terms of initial-state momentum distributions and provides a new tool for the study of SRCs using lepton-scattering reactions.