The situation is when you have a SCORM file (zip) in a course and another course uses this file via an alias/shortcut.

1. Set up the SCORM activity with the source file and another SCORM activity in a different location with an alias/shortcut to the source file.

2. Update the source file by dragging a new file with the same name into the file section of the SCORM activity, choose to Overwrite the file at the popup confirmation.

3. For a few moments, it looks like everything is fine (perhaps 30 seconds).

4. After a few moments, there is no longer a dependency showing in the source file and the dependent activity now has the alias converted to a true copy of the original source file.

Expected behaviour when Overwriting a file with the same file name is that all alias are preserved and the updated material can be seen in the SCORM activities that use the alias.

Moodle docs also supports this expected behaviour:

https://docs.moodle.org/39/en/Working_with_files