Hi fgiorgi ,
Thank you very much for your post.
ATUM Multi-Inventory premium add-on lets you add any inventory into the order and automatically adds the lot/batch according to your store rules.
However, we do not yet work with any invoice generating feature so we are not sure if your invoice plugin handles the MI data or not? We plan to work on this later this early or early in 2021 as ATUM will be fully complaint with any ISO regulations or as you say USDA/FDA when completed.
Hope this helps.
Pavel