This is a really common question which in previous versions was seemingly impossible unless you knew SQL really well. Well in Lync Server 2013 it’s a very different story and you can now use PowerShell to remove content from a room. I am just now waiting for someone to write a scheduled script to run this command with the right date set. If someone has something like this already written please let me know if your willing to share.
Extracts from TechNet:
Removes all the content from a Persistent Chat chat room beginning with the oldest item in the room and continuing through the specified end date. This cmdlet was introduced in Lync Server 2013.