I’m just curious because in the rules it says no emulators, but when you submit a run, there’s a checkbox that says “emulator”. Can someone clarify this for me? And if it’s not allowed, why?
It's allowed for single stars, but not for stage RTA. Technically both of those fall under IL's (depending on whether or not you quantify stars or stages as 'levels'). Assuming you are referring to the submissions on this website, (single star records are not stored here on speedrun.com) which are the stage RTA boards, then no you can't use emulators.
If you wish to replace your twitch highlights with reuploads, please edit your already verified run rather than deleting the verified run and making a new submission. This makes it a lot easier for us to track which submissions are reuploads and should be less work on your part as well.
If you need
