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After you file
" But, I had no idea that my 2018 return was never acknowledged by the IRS!" Not sure what you mean by that. You say you had to use "zero" as an AGI--when a tax return is filed late or amended , often the AGI does not make it into the system in time for you to use it when you want to e-file the next year, so you have to either try using zero or print and mail the return. It is not clear from your post which you ended up doing. You say that you have a canceled check--was that the check you wrote to pay your federal tax due? If so, that is your proof that you paid, and the only acknowledgement you will get from the IRS for paying. What is the date on the check? Was it payable to the United State Treasury? Does the amount match the amount of tax due as shown on your Form 1040?
If you are worried that the IRS did not credit your payment , look at the transcript of your 2018 return that you can get for free from the IRS.
You can get a free transcript from the IRS:
https://www.irs.gov/individuals/get-transcript