Unfortunately Outlook's Cleanup Folders & Subfolders
functionality doesn't work on the Lync / Skype for Business Conversation History folder because the conversations aren't included in the same "thread".
I used the following program to help me do the cleanup. It sure would be nice if it was built into Outlook's Cleanup Folders
logic.
http://www.craig-tolley.co.uk/mini-projects/microsoft-lync-conversation-cleanup/