The issue seems to be that the Builder generated script is not explicitly closing the connection at the end of the experiment so in the case of eyelink, the .edf file is not transfered.
As a short term fix, add a line of custom code to the end of your experiment to close the eyelink connection and transfer tthe file:
eyetracker.setConnectionState(False)
The .edf file should be saved to your experiment data directory with the same name as your other data files, but with the .edf ending.
Thanks again