You are using M$ Windows right I suppose?
I guess M$ Windows does not allow duplicated files at all........something like mugen.exe, you cannot have two (2) mugen.exe files in the same folder.....
If you are talking about one (1) mugen.exe in folder A and another one (1) mugen.exe in folder B then I think you might just use the M$ Windows Windows Explorer search function to search for all mugen.exe files in any different folders........or you can use some other M$ Windows Windows Explorer alternatives I believe you can easily find some in the great sea of the Internet......