This is for future reference to help anyone using the IEdmAddInMgr5 to update existing add-ins.
The method AddAddIns installs add-ins in SOLIDWORKS PDM Professional.
To use the EdmAddin_ReplaceDuplicates, please call the AddAddIns method like this:
EdmAddIn5Mgr::AddAddIns(filePath, (int)EdmAddAddInFlags.EdmAddin_ReplaceDuplicates +EdmAddAddInFlags.EdmAddin_AddAllFilesToOneAddIn, null);