The fate of an Inquisitors agents depends on the nature of the work the Inquisitor investigated and what those agents did before they were members of his retinue. Agents who work for Inquisitors whose job investigated known heresies were likely shared with other Inquisitors who did similar work. Mindscrubbing is a last resort since among the Inquisition, knowledge is power.
Throughout their career, Inquisitors will form their own cadre of agents of various roles and functions in order to achieve whatever goal is put before them. These agents fall into two classes, known as Acolytes and Throne Agents. Acolytes are initiates into the Inquisition's service who may eventually become Inquisitors themselves one day if they perform well and please their master; Throne Agents are mature Acolytes who have served the Inquisition and a particular Inquisitor for years and sometimes decades. They are among the most powerful beings in the Imperium of Man after an Inquisitor himself. REF: Warhammer Wikia -> Inquisitor
There are several places an agent could come from including:
Acolytes: The most common source of support agents are usually younger, less well trained members of the Inquisition. These younger or less experienced agents will learn at the hand of a senior Inquisition member. If said leader is killed or if the leader is less than pleased with their service, they are returned to the pool of available agents for the next Inquisition leader to request.
Throne Agents: Are often other highly trained members of the Imperium who may have jobs doing other duties including priests of the Ecclesiarchy, Astropaths, Servitors, Tech-priests of the Adeptus Mechanicus, etc. Others may be more subtle and even serve a more specific role, such as high-ranking members of the Administratum, the apprentice Inquisitors called Interrogators, elite members of the Imperial Guard like Storm Troopers or the Adeptus Arbites' Judges, and the highly-trained Assassins of the Officio Assassinorum. If they Inquisitor they are working for dies, they simply return to their previous duties.
As far as choosing new agents to work with a particular Inquisitor:
- Ultimately, the matter is left to the judgement of the individual Inquisitors who are subject only to the scrutiny of their peers, as is the case in most matters. A majority of Inquisitors typically leave such matters to chance or perhaps to Fate in regards to picking a suitable candidate from amongst the groups of individuals whose paths cross that of the Inquisition. There are a number of Inquisitors who are more rigorous in regard to the pursuit of Acolytes and will spend a proportion of their time seeking suitable candidates -- often from the ranks of other Imperial Adepta.
The death of an Inquisitor is an undesirable circumstance. In the event an Inquisitor is killed, Acolytes and Throne agents will undergo a rigorous interrogation to understand what happened to a valued agent of the Imperium. This is also to prevent infiltration or espionage by alien or heretical agencies.