Clearing the C:\inetpub\temp\apppools folder should not cause an application to shut down or stop working by itself. However, as I mentioned earlier, deleting the contents of this folder may temporarily impact the performance of your applications as IIS will need to regenerate these files when they are accessed for the first time.
If you are experiencing issues with your application after clearing the C:\inetpub\temp\apppools folder, it's possible that the issue is unrelated to the folder clearing operation. You should review any error messages or logs related to the application and/or IIS to try to determine the root cause of the problem.
It's also possible that the application pool itself was stopped or restarted as part of the folder clearing operation, or that some other change was made to the IIS configuration that is affecting the application. Again, reviewing logs and error messages related to IIS and the application may help you determine the cause of the issue.
If you are unable to determine the cause of the problem or resolve the issue on your own, you may need to consult with a qualified system administrator or other IT professional who can assist you with troubleshooting the issue further.