I just tested on my side and was able to successfully LiveSync a hybrid application deployed on device. This said, can you please share some more information about the issue you are experiencing? For example, do you try to LiveSync in the AppBuilder Companion apps, or the project is deployed as an application package on your devices? Further, does the problem occur only for a specific platform (iOS, Android, WP8), or it happens on all device platforms?
Thank you for your help in advance. I am looking forward to your reply.