When CAD files are migrated to Windchill, there are two cases of filename conflicts. One is conflicts happen among CAD files to be migrated. The other is contflicts happens between CAD files to be migrated and EPMDocuments already exist in the target Windchill. The former conflicts can be detected by CAD Metadata Extractor...which is a part of WBM. But the latter can not be detected by any WBM check tool. As of today, Method server reports such a conflict when CAD files are actually loaded to the target Windchill.
WBM provides some good tools to validate. It should provide a tool to check filename conflict before loading CAD data.