You are the Office 365 administrator for your company.
You need to configure Microsoft Lync Online to disable alerts for voicemail and instant messages to Windows
Phones.
What should you do? mobile application is inactive. Push notifications notify a user of events such as a new or missed IM invitation and voice mail. You can enable or disable push notifications for Windows Phone devices by using either Lync property to False ($False). For example: https://technet.microsoft.com/en-us/library/jj688162(v=ocs.15).aspx

A.
In the Lync admin center, disable public IM connectivity.

B.
Use the Set-CsPushNotificationConfiguration Windows PowerShell cmdlet.

C.
Use the Set-CsOnlineUser Windows PowerShell cmdlet.

D.
In the Lync admin center, select the Display presence information only to a user’s contacts option.

Explanation:

Push notifications, in the form of badges, icons, or alerts, can be sent to a Windows Phone even when the

Server 2013 Control Panel or Lync Server 2013 Management Shell.
To disable push notifications for Windows Phone set the value of the EnableMicrosoftPushNotificationService
Set-CsPushNotificationConfiguration -Identity “site:Redmond” -EnableMicrosoftPushNotificationService $False
References: