Editing a freeform submission entry
It looks like setFormFieldValues() has an optional second parameter related to overriding values...
public function setFormFieldValues(array $values, bool $override = true)
So, changing...
$submission-&gt;setFormFieldValues(['customField' =&gt; $customFieldValue]);
... to...
$submission-&gt;setFormFieldValues(['customField' =&gt; $customFieldValue], false);
may help with the override issue.