If you are reporting income on business entities, you have errors. Too many errors in a key column (I believe income is a key column) and you could be cited, have to scrub and re-file your HMDA LAR (up to a couple of years prior), and possibly be fined depending on how everything else on your HMDA LAR looks.
You need to call Jack Henry and find out how to report NA income. It is possible that the system will convert anything less than $500.00 to NA. But you should definitely call them and find out.
I can't herd the cats anymore, so I just set up the electric fences and let them fry when they stray out of bounds.