Are you using search paths? In config.pro, there are two related options. search_path is the path to the folder on your hard drive. You can have as many of these search_path statements as you need. However, Pro/ENGINEER performance degrades as the number of paths goes up.
If you have a large number of paths, they can be saved in a separate file. In the config.pro file, use search_path_file option to tell Pro/E where the search path file resides.
Also be wary of placing files with the same name in different folders. Pro/ENGINEER will run through the search paths and use the first matching file it finds. If you have different versions of the same file or different files with the same name in different directories, it may grab the wrong file.
When Pro/INTRALINK is being used, these options aren't used.