Performing a back up of the file store has to be one of the easiest parts of the Lync infrastructure. If the deployment is an Enterprise version, odds are that the file store is already on a file server that is regularly backed up. However, if there are Standard Edition servers in the deployment, the file store is probably on the Lync Server, and there might not be any file back up on these servers.

The best solution is to have a backup agent configured and running on each server where there is a file store configured. However, be aware of resources when planning for this and consider only off-peak backup times.

The backup solution described here will just show you how to make an xcopy of the files to a second location for safekeeping.