Indeed, we are still facing problems when live-syncing with the NativeScript companion apps. Though we have the Hybrid companion app working properly, there are some specifics with natively built applications we are still trying to figure out how to handle the proper way.
By the way, did you try restarting the companion app? Sometimes it does sync the code, but it fails restarting after that (which is needed for native binaries to get reloaded).
Check out the Telerik Platform - the only platform that combines a rich set of UI tools with powerful cloud services to develop web, hybrid and native mobile apps.