Then I noticed that the pages had both the "helperphp" files for UE4's file manipulation and the older DFP2 helper file. So it was adding the new reference, but not removing the older one.
So I simply deleted this line.
<?php require_once("../../WA_DigitalFilePro/HelperPHP.php"); ?>
and it cleared things up as far as I can see.
Is there something else I missed that would fix this? Am I updating things incorrectly?