Hi Samuel,
We have experienced the same issue you describe. Each time you restart your Development SMP server the WM version would revert back to the last Zip version of the application loaded via the Admin Console.
After each server restart we would need to republish from eclipse to get the latest changes.
Another workaround was to manually create the folder structure without defining the Agentry Application in the SMP Admin console:
<SMP Install Dir>\Server\configuration\com.sap.mobile.platform.server.agentry.application
Then copy the application files/folders under into that directory and restart the server
Then going forward, after making enhancements to your Agentry app and you didn't need to re-publish from Eclipse after each server restart.
Cheers,
Stephen