I can’t tell you how many clients I’ve walked into with Microsoft Lync 2010 and 2013 already deployed who aren’t performing proper backups. I can tell you that it’s 100%. It seems that a lot of people just don’t know and a lot of consultancies out there really aren’t communicating the proper methodologies. People are relying on SQL backups and virtual machine copies and to be honest, these may not cut it. Worse, they may simply not be supported. For anyone with Microsoft Lync, I’d suggest reviewing the TechNet article titled Backing Up and Restoring Lync Server 2013. It outlines the supported methodologies for backup and restore and includes the PowerShell commands to do so.
The best way to execute these commands are within a PowerShell script within a scheduled task. While the one we use at my firm is highly modified and not publicly available, I can recommend Lasse Wedø scripts which are available for download from the TechNet Gallery. Occasionally these scripts can have difficulty with multiple pools, but are easily modified to avoid this pitfall. Links are below.