Steps to replicate the bug:
1) Add a resource of type file into Course A by uploading a local file from your PC.
2) Add a resurce of type file into Course B by selecting the file you uploaded above from the Server File repository (be sure to identify the resource files of course A) and chosing the "Create an alias" option instead of copying the file. This way the file in Course B will be an alias to the original file resource in Course A.
3) Return to Course A and update the file by uploading the new version of it with exactly the same name and choosing the "overwrite existing file" option when prompted.
4) Now check that the file appears updated in Course A but not in Course B.