yeah i can guess it takes some effort to move save files. And speedrun takes time too.If you own it on Steam yet never played it on there but have played the non-Steam version... then yes, you'd be starting from scratch. There's a detailed writeup on the mod's OP that describes the process of swapping saves/persistents back and forth but it's a cumbersome process for average folks tbh... that's not an insult... feel free to do what you wish but that is the real answer to your question.
i'd rather wait a couple hours.
I hope it's a couple hours instead of 24+lol