soundslike it is leaving the require once line to include the old data Assist helper file:
WA_DataAssist\WA_AppBuilder_PHP.php
remove the require once line that references:
WA_DataAssist\WA_AppBuilder_PHP.php
and leave the one for the webassist\database_management\wa_appbuilder_php.php file, it sounds like you are commenting out the new one:
webassist\database_management\wa_appbuilder_php.php