They will be extracted in a new line as normal text. It will be the last line.

So I’m left to manually link them up?

Have you considered using something like Pandoc’s method of marking them up? Footnotes are a fairly common part of scanned pages, and markdown that doesn’t indicate that a footnote is a footnote can be fairly incomprehensible.

I am lazily posting this all over the thread, but do check out MyST Markdown too! https://mystmd.org. We handle footnotes as a structured object.