High current plasmas in the RFX-mod experiment are characterized by a 3D helical magnetic topology where internal electron transport barriers, with a temperature up to 1.2 keV, develop in the core. Power balance and heat transport analyses have been performed for the first time using high time resolution electron temperature Te measurements obtained by a double filter technique with a multichords soft-x-ray (SXR) diagnostic. Te profiles are implemented in the heat transport equation in order to determine the electron thermal diffusivity across the helical magnetic surfaces assuming both stationary and dynamic conditions. In order to explain the discrepancy between the experimental thermal diffusivity at the barrier and the lower neoclassical predictions, the role of residual macro and microscale magnetic stochasticity on the temperature gradient is investigated. The fast termination of helical structures, analyzed by a statistical approach, reveals the different time scales involved in the dynamics of magnetic and thermal plasma properties.