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 the duplicate files (i.e. files with the same name but different Salesforce file id).

Goto: About page of Mass File Download app 

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

NOTE: You will be prompted to refresh the already opened tab if any.