Whenever an IRS agent via phone or meeting states a position of the IRS, it typically means that is the most updated stance they hold on the matter. IRS letters can often arrive 30-45 days after a decision has been made, favorable or negative, on the matter which counter-state the previous decision.
For example, an agent can re-assess a tax filing and abate a penalty; however, a letter may still arrive after this decision while stating one still owes the penalty. The easiest solution is to call the IRS and verify that the letter's position is no longer held by the agency. In short, the letter may be a delayed (and automated) system-response that was already in motion before a manual decision was made.