I just started TurboTax Self employed, then realized I need to use TurboT Business for a 1041. Do I need to start over and use only the business version?

"Do I need to start over and use only the business version?"

Yes, but you actually need both versions; TurboTax Business can only be used to prepare income tax returns for entities (such as 1041s for trusts/estates). Therefore, you need TurboTax Self-Employed (or a similar product) to prepare your personal income tax return.