Deleted documents are, as far as the Load process is concerned, still present in the ITP/MDK Repository and they will trigger the Document exist pop up. Files are compared by name. So if you rename a file in the ITP/MDK Repository the same file will be loaded under the original name and the Document exist situation will not be triggered.
The target folder is the folder in which the file will be located after the Load action in the ITP/MDK Repository. This can be a folder that is loaded while containing the file. This is important because the duplicate check is on folder level and not on ITP/MDK Repository level.
Documents that are loaded will be locked on behalf of the current user. A warning will be issued if the user already has documents locked that are to be loaded.