Please Note: 

This feature allows you to download files with the same name. If this feature gets disabled, you will not be able to download duplicate files (i.e., files with the same name but a different Salesforce file id).

Go to the About page of the Mass File Download app - 

  1. Scroll Down to the File Download Configuration Tab 
  1. Disable "Rename Downloaded Files for Deduplication".
  1. Click "Save" to update the settings. 

Note - You will be prompted to refresh the already opened tab if any.