Hi,
Is a file of the same name in the destination directory for the upload to the server? By default, you should be asked whether to replace a file of the same name when you start the upload if this is the case, but I assume you aren't getting that message. So, either you need to change directories on the server to where the file should be uploaded, or you have a sub folder selected on the server side and the file is being uploaded to that sub folder. In the latter case, de-select the sub folder.
Of course, you can also edit the file directly on the server, if it's any easier.
Let me know how it goes.
-Jason