Will redirecting my domain affect my Web site's search engine rankings?
Search Engine crawlers view subdomains as independent sites, and will not properly rank your primary domain if it is redirected to a subdomain and contains no content. You should avoid redirecting your primary URL to a subdomain, and instead create content for it or setup Search Engine Visibility V1 for your subdomain.
For example, if my primary domain is www.coolexample.com, and I also have www.store.coolexample.com. For Search Engine Optimization purposes, I should not redirect www.coolexample.com to www.store.coolexample.com.
If you move files or need to move your Web site to a new domain, 301 redirects are the preferred method for preserving search engine rankings. For details on using a 301 redirect, see Using 301 Page Redirects.