The BiBatchConverter Server Service can be configured to overwrite the existing document.
The BiBatchConverter Server Service Manager has an Configuration option to configure the Service settings.
Start the BiBatchConverter Server Service Manager
Click on the Configuration menu option
Check the “Overwrite output document if the document already exists with the same name in the “Converted Folder”” checkbox and click OK
Start the conversion, the documents with the same name will be overwritten if the document already exists with the same name.