It has happened to all of us at one point in time or another.
I know you said you already apologized to them but did they open a dispute? If they opened a dispute and it was in their favor they were already reimbursed by ebay for their fee's.
But if they went ahead and relisted without opening a case, honestly that is sorta their problem. And I wouldn't fret over owing them the fee's. The dispute process is only four days for them to wait to get their fee's back, it's not like it's a month.
It's nice that you want to make it right but like I said I wouldn't fret if they did not open a dispute.