We don't have to run any report at the end of the year (that I know of.) We simply keep a hard copy in a binder that documents each month's bean purchases, single origins roasted/sold and specific components of blends sold.
There is no keeping track of what is in or out, as far as I know. We simply track the different single origin beans roasted each month as well as the blends, as noted above. The single origin retail packages have the original organic lot numbers listed after the bean name and coop/estate and the blends carry the lot number we assigned each specific batch. ("Mexican Altura, Chiapas - Porvenir Coop - Medium Dark Roast, Lot #208/6372/009" for a single origin, "Heart and Soul Blend, Lot #2, Beans from the Americas and Africa," for a blend.)
The USDA basially wants to be able to follow a bean from the time it arrives in the shop when it is sold. That means if someone has a problem with a bag of beans they buy, it is relatively easy to look at the label and cross reference the binder to see which lot/lots of beans are being scrutinized. For example, right now our Ju-Ju blend #3 is on the shelf of a local health food store. Our records will show which single origin beans currently go into the recipe of the blend in question.