My IT department tells me they want to transfer my main site domain, which has been in existence since 1999 as an e-commerce site (maindomain.com) to a sub-domain (www2.maindomain.com) or a completely new domain (newdomain.net). This is because we are launching a new website and B2C e-commerce engine, but we still have to maintain the legacy B2B e-commerce engine which contains hard-coded URLs, and both systems can't use the same domain.

I've been researching the issue across SEOmoz, but I haven't come across this exact type of scenario (mostly I've seen a sub-domain to new domain).

I see major problems with their proposal, including negative SEO impact, loss of domain authority/ranking and issues with branding.

Does anyone know the exact type of impact I can expect to see in this scenario and specific steps I should go about to minimize the impact?

Btw, I will be using Danny Dover's guide on properly moving domains where appropriate.

Thanks!