Hi,
This is how I do it.
Upload the file using your normal method, FTP etc.
Leave it in the Upload directory and don't try and move it to a category.
Log into into your area using Power Admin mode and click on files tab.
Click List Products on the left hand side.
Type name of the file in the search box and click filter.
Select the file you want to update.
On the right hand side of the page you will see "update with upload". Click this.
Select your uploaded file and click replace.
Then save in the normal manner.
Done
Adam