I don't know how to prevent it. However, you can use a plugin that does file maniuplation and have it check for and delete the file if it exists. There are many plugins that do this, but the Base Elements Plugin from Goya is no-cost license. This would be a solution for FileMaker Pro clients. You can even have the script install the plugin automatically for the clients.
Create a folder there and name it 'Import.log' ?
Removing file can be done as export records with 0 record found set.
One thing to keep in mind: If something goes wrong with the import, having the log around is useful. Either the plugin idea or the export-blank-found-set idea is good when scripted; that way, you can error trap and if your procedure returns anything other than error code 0, you can bypass killing the file.