After you file

Your statement of the principle -- to act in a manner that "assume[s] that you have gotten or will receive the original refund" -- is helpful. I noticed IRS acted in accordance with it when they over-refunded on my 2019 return (what is it now?) 2 years after I filed the amended return and then they billed me for the difference in the two tax amount (no penalties, thank goodness).

I will file the 1040X now and send in the additional tax. Then things will be even when they finally (in 2023?) catch up with themselves and send me my original refund.

The 4464c letter was very non-specific as to what the items they needed to verify were ("income, income tax withholding, tax credits, business income"), so it is hard to know what they had in mind.  I hope this will satisfy them.

Bill