It looks like there is an option within camel FTP, which QIE uses (see http://camel.apache.org/file2.html).
Try adding the following Custom Apache Camel parameter:
fileExist=Append
See the following example:
I am unsure of the performance of this option. If performance becomes an issue, I recommend appending to the file locally, and then uploading the file with a separate channel at a certain interval.