The instant crystallization of semi-crystalline polymers has become possible following the recent advances in Fast Scanning Calorimetry (FSC) and enables us to make a bridge between the time scale available experimentally with those accessible with computer simulations. Although the FSC observations have provided new information on the crystallization kinetics and evolution of the crystals, the molecular details on the chain exchange events between the ordered and disordered domains of crystals have remained elusive. Using molecular dynamics simulations, we examined the detailed chain dynamics and thermodynamics of polyamide 6 (PA6) system under two heating treatments: (i) quenching PA6 melt deeply below the melting temperature Tm and (ii) annealing the resulting quenched system to a temperature close to Tm. We categorized the chains into mobile amorphous fraction (MAF) and rigid amorphous fraction (RAF), based on the length of consecutive chain's bond angles in the trans state. In the deep quenched system close to the glass transition temperature Tg, the mobility of the MAF chains is strongly suppressed and they remain in the glassy state. However, upon rising the temperature close to melting temperature, the system undergoes recrystallization, leading to the coexistence of RAF and supercooled liquid MAF chains. The highly mobile unentangled MAF chains explore the interphase domains, and during the late-stage of crystallization, they are thermally translocated into the lamella by reducing the fold number of RAF chains. The chain mobility in the annealed system could potentially lead to improved biodegradation in semi-crystalline chains.