Editing a freeform submission entry

I have a custom plugin where I get a freeform submission by token. I woud like to change a value in this submission and resave the submission. When I try this the old form data gets overwritten.

$submission = Freeform::getInstance()->submissions->getSubmissionByToken($submissionToken);

$submission->setFormFieldValues(['customField' => $customFieldValue]);

// method 1, doesn't accept type submission, should be form     
Freeform::getInstance()->submissions->storeSubmission($submission);
// method 2, old data get's overwritten, current submissiontoken changes
Craft::$app->elements->saveElement($submission);