Hello,
Sorry for the late reply, we have been under a great load of work.
I can't really guarantee what it's happening in the third party application, still, when developing with Bluetooth LE in Android as far as my investigations went, there are two ways to disconnect a device with two different methods, so I'm not sure which one your mobile application uses.
I believe that what you will need to do or are trying to do it's to create your custom profile, and you are more likely to be looking for the unsubscribe functions in the SDK.
You can check for example the heart rate sensor example and look for the battery service, in the battery_service.c you will find a function called Bas_Unsubscribe.
Could you please check it and let me know if that it's helpful for you ?
Regards,
Estephania