The files remain on the file store until they are deleted by the meeting organizer or they are removed by Lync at the default time period of 15 days (after the meeting). The default time period is configurable and can be set to any value between 30 minutes (00:30:00) and 180 days (180.00:00:00).
To view the current setting, open the Lync Management Shell
and view the ContentGracePeriod attribute using this command: Get-CsConferencingConfiguration
To change the value, use this command: Set-CsConferencingConfiguration
-ContentGracePeriod <value>