I agree with you...but it sounds like maybe this e-file was transmitted without approval and without signing the 8879's? Although well-intentioned (trying to get client her refund fast by making deadline) this would still technically be the ERO's mistake. If my assumption of what happened is correct, it is still ERO/preparers's fault for sending whout authorization....So maybe a refund is in order.
HOWEVER....If she instructed you to transmit the reviewed return and signed the 8879, then as others have suggested...no refund of fee.
To answer your question...No, you cannot retract the transmitted e-file....She will have to amend and mail in the amended return. If her father's choice of preparers is honest, her "revised" return should be the same and you will never hear a complaint (or a thank you) from them. If, somehow, a dishonest preparer amends to increase a refund...then they deserve the audit that they will hopefully receive. In the end you will be proven right.