In this work, we present an experimental study of the primary and secondary relaxations of the semi-crystalline polymer polyethylene naphthalate (PEN), by Modulated Differential Scanning Calorimetry (MDSC), Thermally Stimulated Depolarization Currents (TSDC) and Broadband Dielectric Spectroscopy (BDS), and how they are affected by physical aging. Three dipolar relaxation modes can be observed: (from slowest to fastest) the primary $\alpha$ relaxation, which vitrifies at the glass transition temperature, $T_{g\alpha}$, and two secondary relaxations, named $\beta^*$ and $\beta$. MDSC results show how the secondary $\beta^*$ relaxation also vitrifies, giving rise to an additional glass transition at $T_{g\beta^*} < T_{g\alpha}$. In fact, the $\alpha$ and $\beta^*$ relaxations can be considered as part of a very broad and distributed relaxation. Its main part is the primary $\alpha$ relaxation with a shoulder at the high-frequency region corresponding to a complex secondary $\beta^*$ relaxation. BDS results about the $\beta^*$ can be modeled by a main contribution ($\beta_3^*$) and two additional ones ($\beta_1^*$ and $\beta_2^*$) with a weaker dielectric strength. TSDC results show that each single mode of the relaxation has its own glass transition temperature and they are compatible with the structure inferred by BDS. This scenario gives rise to an extended glass transition dually centered in the $T_{g\beta^*} \sim 305$ K and $T_{g\alpha} \sim 387$ K. temperatures.