I opened an HSA account, then closed it 2 weeks later. However, a bank transfer of $3350 went through anyway. After my refund, do I still owe a 20% penalty?

When I realized the transfer went through, I requested my money to be refunded, and it took 3 months to get it back (actually $3320 came back since the index funds lost money). Then I received a form 1099-SA from the HSA bank. It's over the 60-day limit now, but I did deposit the same amount of money ($3350) in a new HSA through my employer.