WP Media Overwrite

WordPress does not overwrite files that have the same name. Instead, it appends a number or random value at the end of it to make it unique:
filename.png will be turned to filename-1.png

If you do not want that, this plugin is for you. Instead of adding it as a separate file, it will replace the file if it is within the same folder.
Here’s a list of all the available features:

Features

• Overwrite files that have the same name within the same folder
• Compatible with Windows Azure integration and other plugins
• Custom setting to automatically copy the data from the old file (Title, Caption, Alt text, description, metadata)

PLEASE NOTE: After a file is replaced, the old file is still visible within the media window. Once you refresh, it is gone.