Currently the plugin will clean the destination workspace before the cloned workspace is copied there. This is problematic when the job uses the Multiple SCM plugin in to get another set of sources, even if set up correctly this leads to a complete checkout of all of the other sources for each invokation of the build.
I guess allowing the user to choose to unzip the cloned workspace into a directory and to only clear this directory before copying might solve the problem.

While one might argue that such an option might be better located in the multiple SCM plugin, other SCM plugins like SVN offer such an option. (Besides this option could be useful if cloning workspaces from more than one job will be possible)