In short, no it won't.

If you're following best practices in terms of opt-in process, are following good list hygiene practices, AND you're providing engaging content, then your sender reputation score should go up over time with consistent sending. Whichever of the two domains had the most engaging content and consistent sending patters will enjoy the best deliverability and inbox placement. If you have certain content that is not as engaging as other, mixing it up helps get the less-engaging content delivered.

If you separate the engaging content from the not-engaging content, then one will enjoy good deliverability and the other will not. Deliverability and spam filters are ALL about engagement. There is no cheating them or tricking them.

Its important to remember new domains should be "warmed up" first to give the email service providers time to see you coming. Send regular small, incremental batches of highly engaging content. If the email confirmations are opt-in confirmations, then these should grow organically as your list grows reducing the need for a warm up.

Feel free to schedule a call -- I can give you more specific help if I know more about your situation.