They won't be, because Nintendo recognizes that that would be a bad idea for speedrunning, and this game is designed for speedrunning. (As for what if, I have no idea)
This is an issue we should worry about now! Another game called Cuphead recently had all the main glitches patched out and they cleared the entire leaderboard in confusion about what to do.
We should come up with a different better strategy now, so if or when that happens we won't be in complete chaos here.
I would personally think having an have extra sub categories for before patch, with the current patch being the main run category. This would be similar to how Assists / No Assists currently work, with the only difference being you would have to select the patch you are playing on.
We would switch back or stay with the original patch, easy.
Only problem would be if the people that updated couldn't revert back-in which case, they're fucked.
The question is, how easy is it to just play without a patch? If that's easy then there's no reason to create a separate subcategory for versions since everyone could just play on the old version without any problem.
If the patch is easily reverted through Switch settings then we can all just run on the same patch. If the patch is not easily reverted (without hacks) then the only option is to archive the leaderboard and start over. It sucks but it is literally the only option.
