Footnote numbering restarts at one between unthreaded text boxes

I am creating an accessible PDF in InDesign, which means that text boxes cannot be threaded as it interferes with the remediation process. Normally I create the document with threaded text boxes and then run splitscript to break them up. However, this document has hundreds of footnotes. When I break the text boxes it restarts every single text box's footnotes at 1. I need them to continue from text box to text box, but I can't seem to restart the footnote numbering at a certain value within each text box.

How do I get around this? Accessible documents is the law in my province (Accessibility for Ontarians with Disabilities Act) so I can't just throw my hands in the air and decide not to do it.