APPROVED ANSWER
replied on January 6, 2015
If you use the new XML list format, then you can control the action that occurs when there's a document name conflict.
I'd recommend reviewing the ImportEngine.xsd file located in the "List File Examples" folder in the Import Agent installation directory. After getting a handle on the XML schema definition, you can further use the example .xml files in that same folder to see how things work. For your scenario, see this example:
<?xml version="1.0" encoding="utf-8"?>
<LF:importengine xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://laserfiche.com/namespaces/importengine ImportEngine.xsd"
xmlns:LF="http://laserfiche.com/namespaces/importengine" version="1.0">
<LF:toc on_document_conflict="overwrite" on_folder_conflict="unique">
<LF:document name="Transportation" comment="" language="" template="">
<LF:electronic_document content_type="application/pdf" extension="pdf">
<LF:fileref ref="C:\Temp\sample.pdf" />
</LF:electronic_document>
</LF:document>
</LF:toc>
</LF:importengine>
The thing to notice is the setting
on_document_conflict="overwrite"