You must turn on option "Append to existing file" in section  "FTP settings" (inside the job).

The plugin will download existing file and pass it to "hook" function.

So you have to add following PHP code to section "Misc Settings" (inside the job too!).

Probably you should tweak this code a bit.

add_action('woe_ftp_append_CSV',function ($existing_file, $new_file) {
  // read new lines
  $lines = file($new_file);
  // remove first line - you don't need following code if your CSV doesn't have header
  // kill extra line breaks? 
  $lines = array_map("trim", $lines); 
  //append new lines to existing file 
  $result = file_put_contents($existing_file, join("\n", $lines)."\n", FILE_APPEND);
  //replace file for upload
  copy($existing_file, $new_file);
}, 10, 2 );