Sort by the number, not by the worry.
A Form 1120-S notice can ask about a figure, show a balance, or propose a change. Those are different jobs. The notice number is public, and the agency publishes a plain description of what that number means. We start there. The tone of the page is a poor guide, because a balance due and a proposal can look equally stern.
Owners sometimes hear the word examination the moment a notice arrives. Some numbers really do open that kind of review by the Service. Many do not. Treating a proposal as an examination spends the month on the wrong file. We say which kind of mail you are holding, in ordinary words, after we see the number.
One common notice proposes a change to income or to a payment and asks for agreement or a response. The worry is that the page is a class you were supposed to have taken. We read it against the closed month and the return that was filed, and we tell you whether it is a change you can answer from the books. The next step is that response, written from the month the bank already matches.
If the figures on the proposal do not match the books you trust, the response starts with those books. If the books were never closed, the response is not ready, and we say that. An open month is a weak answer to a specific notice.