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Ryan, AppDynamics Community Manager
Would you be able to provide more information?
The Java Agent is added to the startup of the Application it's instrumenting, so a server restart would not affect the agent, as when the application starts , the agent will start with it.
Can you validate that the Appdynamics Java Agent is still part of the Application Java Process, you can check using any command e.g ps aux | grep "javaagent".
It might be possible that the following occurred
1. Java Agent directory itself was removed, or permissions changed with patching
2. Server firewall turned on, blocking the Java Agent from communicating to the Controller
3. Application was patched, which removed the Java Agent startup parameters.