I have COSMOSWorks installed as well, and I just found a COSMOS Cleaning Utility in my install directory (C:Program FilesSolidWorksCOSMOSWorksUtilities) - the associated help file describes describes it thus:
"The COSMOS Cleaning Utility is a utility program meant to clean SolidWorks files of the COSMOS data they may contain. In particular, the COSMOS Cleaning Utility lets you choose which COSMOS data you want to delete among: COSMOSWorks data, COSMOSXpress data, COSMOSMotion data, COSMOSFloWorks 2008.