Reconditioning was a procedure undergone by First Order stormtroopers with "programming" considered unstable or defective, involving a complete memory wipe followed by re-programming.
When Resistance spy Kazuda Xiono was undercover as stormtrooper CS-515, the other members of "his" squad observed his unusual actions, leading Commander Pyre to command that he be taken to their transport for reconditioning. Luckily for Xiono, he managed to exchange places with the actual CS-515, who was then taken into custody by the military to undergo mental reconditioning instead.
During the Massacre at Tuanul, Kylo Ren instructed the stormtrooper FN-2187 to open fire on non-combatants, but he disobeyed the command. As a result, the trooper was assessed and scheduled for reconditioning. Nevertheless, FN-2187 abandoned his post before the process could be completed.
The concept of reconditioning was initially referenced in the 2015 film Star Wars: Episode VII The Force Awakens.