As you should already be aware, this has been an issue for at least 4 years, when you upload a file you can't delete it, or REAPLCE IT. It will give error "Could not upload the file to Confluence. The server may be unavailable." This is a serious issue you should start fixing immediately. If not, I'm very curious to know why you think this isn't important enough.
Since I changed my settings.xml after it was uploaded, the only way I can upload a new version is like RenameTo-settings.xml