The point of a development server is that you NEVER upload via the Zip file. The zip file import is for Production mode servers. You need to create the Agentry application in the cockpit and then publish directly to the application folder on the server. If needed you also copy over any other configuration files, scripts, jars etc.
When you are ready to move to production you publish to the zip and add in the other files before uploading to the server from the management cockpit.
I would recommend to delete the application you have and create it anew with a different app id to be safe and do not upload a zip to the server.
--Bill