Recalibration is the process performed on Pre-Cals who have been exposed to banned materials, such as Zager's altered manifestos, or who have been exposed to serious illness from an infected person. The affected Pre-Cal is brought to a detention cell to await Recalibration. The actual procedure is carried out in a highly secure lab on the top level of Terminus. The Pre-Cal is either brainwashed to forget what they should not know, or killed and dissected. A new Mirror is then eventually brought down from the Mirror Lab to replace them: the next clone in the series.
There is typically a "three-strikes" system of punishment. On the third strike, the Pre-Cal is usually always Recalibrated. If the offense is severe enough, a Pre-Cal may face immediate Recalibration, regardless of how many strikes they have.
The fact that the first seven clones in the 390 series (390-A through 390-G) are currently living in the real world outside of Metamorphosis, suggests that there is more to Calibration and Recalibration then what is explicitly revealed. See Post-Cal Theories for more detail on this.