Can you explain in a bit more detail what you are trying to do? What do you mean by an 'alias file'? Which file?
I added a word document in one of my files, and created an alias file for that same file in another course. When I go to update that file by overwriting the current file it gives me that error message, and it won't update the file for me. The picture from the first 'alias' file is the original. The second picture is the file where I created the alias document in.
Unless there's something I don't know about (possible!) this isn't my understanding of Alias files (see https://docs.moodle.org/31/en/Working_with_files#Creating_an_alias.2Fshortcut). If nothing else, the alias should have the little shortcut arrow.
I'm still not sure what you did to correct the 'alias'?