We apply a quantum-mechanics/molecular-mechanics (QM/MM) scheme to simulate the migration of charged defects in alpha-quartz. A QM/MM framework together with a self-interaction correction (SIC) scheme was used to investigate the stability of the charged dimer defect and the E'(1) center in alpha-quartz. The use of a SIC scheme makes the charged dimer center unstable in alpha-quartz, in agreement with the experimental failure of identifying this defect, while the effects of the correction of the self-interaction error on the E-1(') center are negligible. Moreover, we conjecture that by overcoming a low energy barrier, the puckering mechanism (ideally heading from the charged dimer defect to the E'(1) center in SIC-free calculations) can be reiterated allowing the drift of the positive charge localized on an overcoordinated oxygen atom. This process can be regarded as an important channel of structural reorganization of oxygen deficient silica in the presence of strong polarizing electric fields.