Extension Rejected - made a payment, should we re-file the extension before 4/20 or just go ahead and file our taxes now?

We filed an extension on 4/15 that was rejected, so our payment did not go through. We did Direct Pay today to try to avoid any additional penalties and interest. Now I am not sure whether we should bother re-filing the extension or just file our taxes now (two days late). From my understanding, we will still be assessed the late filing penalty either way and we don't really need the extension anymore as we were able to obtain the info we were missing in the meantime.