Not home so I can’t try it but do you need to be so specific to match the whole markdown syntax?
You might be able to get away with
s/#(\w+%20)*\w+\.\w{2,3}/\L&/g; /#(\w+%20)*\w+\.\w{2,3}/ s/%20/-/g
basically, matching #this%20is%20LIKELY%20a%20link.md as opposed to matching whole markdown link
lowercasing that entire match, then on a search matching stuff that looks like that, replace the %20 with a hyphen (combined into a single sed command). this only fails when an http link falls within the same line as a markdown hyperlink
Obligatory notice that they rescinded the memo, but not the action. There is still a pause. The EO on federal funding still remains.