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I found this Knowledge Base Article. Can you see if this helps?
https://community.appdynamics.com/t5/Knowledge-Base/How-do-I-deploy-a-NET-Agent/ta-p/41772
If your app is running in IIS, and you restarted both the agent and the IIS, it should work.
Here are some questions
1. If you are running a machine agent on the same server, please ensure that in the machine agent controller-info.xml you set dotnet compatibility mode to "true".
2. Ensure to generate some load on the IIS application, it will only register the tiers if there is load on them. Easiest way is to just open the browse option for whichever applications you have deployed and clicking through the app or refreshing the base page a number of times.