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Well, the answer is that if it is set up properly, it won't have any effect at all really when it comes to the search engines.
When you have your site published to a subdomain and a custom domain here at Yola, we set up something called a 301 Redirect so that if your subdomain is used, it will redirect your site visitor to your custom domain.
What this also allows, if you currently have traffic that uses your subdomain, if you also publish to a custom domain this will make it possible for people who use either of your domains to get to the proper site.
Please let me know if this does not answer your question.