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what OS are you using and what kind of user is starting the APEX Listener?
Per default, the configuration is stored in a apex -directory below the java.io.tmpdir. On Windows systems, this usually is the users TEMP, which is located in the users Local Settings, but a different location may be configured in the environment variables. On Linux/Unix systems, the default will depend on your distribution and the actual location again on set environment variables.
I can run the APEX Listener standalone without the need to reconfigure it. I only have to do this when the TEMP is cleaned up. Possibly, this is done in your case or the Listener can't even read/write there.
An option to ensure that the configuration persists would be to configure the config.dir parameter in the web.xml to point to a directory that is available permanently. To do that in standalone mode, you have to edit the web.xml inside the war file or unpack the war, edit the file and repack it afterwards.