It is not possible to clean the global "workspace" that holds the SCM workspace information. This is needed as it might happen, that the SCM information might be damaged or out-of-date.
In my special case I have a project that uses SVN externals to a single file. This is not supported if the SVN Workspace Version is lower than 1.6. So I changed the default SVN workspace version setting in Jenkins from 1.4 to 1.6. After that it is necessary to clean the already existing SVN workspace. Yet this is not possible because an appropriate "Button" at the root of the Multibranch Pipeline is missing. In Jenkins 1.0x a job offered an option "Wipe Out Current Workspace" to solve this deadlock.