Agents Brown and Jones continued to work for the Machines at least until the events of The Matrix Online. They were not deleted, they were not in exile, and they were not upgraded and turned into Agent Johnson, Thompson, or Jackson.

Sources: According to Wikipedia, Agents Brown and Jones appeared from time to time in The Matrix Online. Additionally, an independent source in a forum post mentions Agent Brown questioning players in The Matrix Online (full thread here). Unfortunately, there do not appear to be any publicly available videos or screenshots of Agent Brown or Jones in The Matrix Online.

Credit goes to user Richard for the tip in the comments about their appearance in The Matrix Online.

Agents Brown and Jones continued to work for the Machines at least until the events of The Matrix Online. They were not deleted, they were not in exile, and they were not upgraded and turned into Agent Johnson, Thompson, or Jackson.

Sources: According to Wikipedia, Agents Brown and Jones appeared from time to time in The Matrix Online. Additionally, an independent source in a forum post mentions Agent Brown questioning players in The Matrix Online (full thread here). Unfortunately, there do not appear to be any publicly available videos or screenshots of Agent Brown or Jones in The Matrix Online.

Credit goes to user Richard for the tip in the comments about their appearance in The Matrix Online.