@crystico
Yes, go ahead and send your 2019 return to them. Attach a letter detailing the facts you attest to above.
Generally, you'd send a copy of your cancelled check, but a picture should be fine.
Also, send a copy of your bank statement or credit card statement, as the case may be, that shows that your payment had been processed.
What you're experiencing does happen sometimes. Once the IRS receives a paper return with check attached, one of the first things they do is separate the two, processing the check before the return itself.
