the clean server from integration services workbench is the Integrator clean server. applied on an Integrator Synchrony Server, it change all composer configuration commited on this Synchrony server to the checked status, and remove all the configuration from Integrator server.

the clean server in the topography workbench changes all composer configuration commited on this Synchrony server to the checked status, but does not make any action on Integrator server.
it has been renamed "Reset Synchrony Server in Composer" in the topography in Synchrony 4.2 to avoid confusion