Thanks! I needed to cast as a Java string with a particular encoding without interfering with the messages to finish making this work, but now we're getting our file copy and still getting the messages.
var bytesTemp = new java.lang.String(bytesIn, 'UTF-8');
qie.writeFile('D:\\FakePathByLewis\\FakeFile' + qie.formatDate('yyyyMMddhhmmssSSS') + '.csv', bytesTemp, false);
bytesTemp = null;
bytesOut = bytesIn; //to be processed through the channel