I can honestly say that I've never encountered this!
Makes me wonder about the complexity of the form. To be sure I understand, the form template is maintained electronically and contains numbered footnotes. When you execute the form (create a record), you print and sometimes need to apply handwritten footnotes?
It's really all about data integrity. You should just ensure you're complying with the ALCOA principles. Are the (handwritten) footnotes Attributable, Legible, Contemporary, Original, and Accurate. To keep them identifiable, maybe label them as H1, H2, etc. (Handwritten 1)? To complete the thought, to help ensure they are attributable, it's pretty standard practice for the author to sign / initial the (handwritten) entry and date it.