The Silent mode logs - the logs displayed in the console when running the wizard mode - are generated in the launch folder, in a file called Rhp2MDSilent.main.log.
By default, the transformation logs are generated in the user folder (%USER%\.rhp2md\com.sodius.mdw.interop.rhp_md_sysml\logs). They are generated in both wizard mode and silent mode.
It is possible to configure the transformation logs path by setting the "user.home" option in publisher.ini file. For example:
-Duser.home="d:\temp"
You will need administrator rights to update "publisher.ini", if the Publisher for Rhapsody has been installed in default folder "c:\Program Files\"
With the current version of the publisher, it is not possible to configure the path of the silent mode logs.