Was just doing a quick Google and apparently Twitch deletes VODs unless you make a highlight of the specific speedrun. How does that work? Is that like a separate VOD that doesn't delete, and that you can put as a link when submitting runs?

Yes, Twitch deletes stream vods after 14 days automatically. Highlighting the interesting part of the vod (or the whole) prevents deletion. When you highlight a vod a separate video is created. So if you submitted a run with the original vod you should probably edit that submission and insert the link for the highlight.

For info how to create one, see the official guide: https://help.twitch.tv/s/article/creating-highlights-and-stream-markers?language=en_US