Hi ... different expert here with a different answer.
If you;ll look at IRS publication 556, you'll see on page 4 this statement:
"Repeat examinations. The IRS tries to avoid repeat
examinations of the same items, but sometimes this hap-
pens. If your tax
return was examined for the same items in
either of the 2 previous years and no change was pro-
posed to your tax liability, please contact the IRS as soon
as possible to see if the examination should be discontinued-
(...Bottom left side of the page).
I would contact them and reference this statement.
This seems to be NOT ONLY your exact situation, but yet another example of the IRS' right arm not knowing what the left arm is doing.