Instead of the footnote being compiled to correct MMD footnote format, the compiler creates some kind of internal Scrivener link and ignores the text of the footnote altogether. So the eventual Markdown output looks like:
This phenomenon was ultimately a product of the earlier [campaigns.](scrivcmt://CBB7FDE7-D8E0-4D2F-8E55-322ACE9B9D0C)
…when it should look like:
This phenomenon was ultimately a product of the earlier campaigns.[^Smith 1990.]
This broke several months ago and has been intermittently reported, but no one seems to have mentioned it lately. Since we are now at release candidate status I’m uncertain whether there’s some setting in the compiler that I need to change, or whether this indeed remains unfixed.