We analyze the early X-ray flares in the GRB flare-plateau-afterglow (FPA) phase observed by Swift-XRT. The FPA occurs only in one of the seven GRB subclasses: the binary-driven hypernovae (BdHNe). This subclass consists of long GRBs with a carbon-oxygen core and a neutron star (NS) binary companion as progenitors. The hypercritical accretion of the supernova (SN) ejecta onto the NS can lead to the gravitational collapse of the NS into a black hole. Consequently, one can observe a GRB emission with isotropic energy $E_{iso}gtrsim10^{52}$~erg, as well as the associated GeV emission and the FPA phase. Previous work had shown that gamma-ray spikes in the prompt emission occur at $sim 10^{15}$--$10^{17}$~cm with Lorentz gamma factor $Gammasim10^{2}$--$10^{3}$. Using a novel data analysis we show that the time of occurrence, duration, luminosity and total energy of the X-ray flares correlate with $E_{iso}$. A crucial feature is the observation of thermal emission in the X-ray flares that we show occurs at radii $sim10^{12}$~cm with $Gammalesssim 4$. These model independent observations cannot be explained by the fireball model, which postulates synchrotron and inverse Compton radiation from a single ultra relativistic jetted emission extending from the prompt to the late afterglow and GeV emission phases. We show that in BdHNe a collision between the GRB and the SN ejecta occurs at $simeq10^{10}$~cm reaching transparency at $sim10^{12}$~cm with $Gammalesssim4$. The agreement between the thermal emission observations and these theoretically derived values validates our model and opens the possibility of testing each BdHN episode with the corresponding Lorentz gamma factor.
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