Q Is it even worth sending a letter of disagreement with proof of payment in 2020?
A. Yes. That's what's needed, proof of payment in tax year 2020 for 2020 courses. The IRS flagged your return because there was no 2020 1098-T. Include a copy of the 2019 1098-T if it shows box 7 checked.
Q. Does this count for the lifetime learning credit?
A. Yes. Payment must be in the same calendar year as the courses. The one exception is you coulda counted the 2020 spring course, on your 2019 return, if you had made the payment in 2019.
Be sure you didn't already count the full 2019 1098-T box 1 amount on your 2019 return. If you didn't actually pay some of the box 1 amount until 2020, it should not have all been counted on your 2019 tax return.
