One option is to edit posts as you come across them, rather than all at once. This way you can also look them over to see if there's anything else you want to improve while you're there. `<sup>` footnotes work, so nothing's broken now (unlike, say, broken links or missing images). This means there's no rush.
As noted in comments, footnotes don't work right if more than one post on a page uses footnotes, like a question and an answer or multiple answers. We need to figure out how to scope footnote numbers to portions of the page. If you think this is a likely scenario, you might want to hold off on changing those ones to Markdown footnotes.
All edits bump posts now. We've talked about having a way to do minor non-bumping edits, but we haven't gotten to that yet, sorry. "How many bumps at a time is too many?" is a question for the Math community, not staff, so thank you for raising it here.