Okay, I think I can help clarify. The “missing” value code of 99997 applies to the 1976-2010 swap values data file. You are correct that in the income data, all item non-response cases are imputed. This is not the case for the swap values data file. As is noted on this page, “Every non-zero value in the swap values file should replace a topcoded value in IPUMS. All other values are missing or zero, meaning that the income variable is not available for that year or the income was not topcoded, respectively.”