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I was trying to edit the /templates/files.* as you mentioned, the default theme. However, I'm not sure it would have made a difference in which theme templates I was trying to edit the way I resolved the issue.
Here is what I did, without cloning as you mentioned.
1)Found the respective modules/moduleX/templates/files.*
2)Made the changes in ///templates/files.* and saved each file.
3)Then went back into admin CP to system/modules/ and updated moduleX.
Just because the editing is done and saved, it does not mean the actual updating of modules is done. Updating modules, it appears is a manual task.
hsalazar your posting is a good explanation. Coupled with this one, it should help Xoopers.
Happy Easter