After the successful detection of cosmic high-energy neutrinos, the field of multiwavelength photon studies of active galactic nuclei (AGN) is entering an exciting new phase. The first hint of a possible neutrino signal from the blazar TXS 0506+056 leads to the anticipation that AGN could soon be identified as point sources of high-energy neutrino radiation, representing another messenger signature besides the established photon signature. To understand the complex flaring behavior at multiwavelengths, a genuine theoretical understanding needs to be developed. These observations of the electromagnetic spectrum and neutrinos can only be interpreted fully when the charged, relativistic particles responsible for the different emissions are modeled properly. The description of the propagation of cosmic rays in a magnetized plasma is a complex question that can only be answered when analyzing the transport regimes of cosmic rays in a quantitative way. In this paper, therefore, a quantitative analysis of the propagation regimes of cosmic rays is presented in the approach that is most commonly used to model non-thermal emission signatures from blazars, i.e., the existence of a high-energy cosmic-ray population in a relativistic plasmoid traveling along the jet axis. It is shown that in the considered energy range of high-energy photon and neutrino emission, the transition between diffusive and ballistic propagation takes place, significantly influencing not only the spectral energy distribution, but also the lightcurve of blazar flares.