Agents Brown and Jones from The Matrix were replaced by upgraded Agents Johnson, Thompson, and Jackson by the time of The Matrix Reloaded. But what happened to them?
In The Matrix Reloaded the Oracle explains that when a program faces deletion (due to replacement by an upgraded program, for example) the program can choose either to return to the Source for deletion or go into exile.
Many of the exiled programs seen in The Matrix Reloaded and The Matrix Revolutions are programs that performed similar functions as the Agents in previous versions of the Matrix -- we see vampires, werewolves, and ghosts (e.g. the Twins) from the Nightmare Matrix and possibly angels from the Paradise Matrix (the guards at Club Hel can "fly"). Presumably, therefore, it is common for security-type programs like Agents to choose exile over deletion, so that would be my guess.
Is there a canonical source which provides any clues as to the fate of Agents Brown and Jones?