A Google Groups thread asks if having two Sitemaps for the same site will cause an issue with Google. In short, Google said no.
Why does this site have two Sitemaps? Well, the only way for multiple Google Accounts to gain access to the Webmaster Tools verified access to a particular site, is for Google to verify both sites with unique verification codes. In each of those verified accounts, the account holder does have access to upload a Sitemap. In addition, one account holder can upload more than one Sitemap.
In any event, Google does not frown upon multiple and duplicate Sitemap submissions. Google said, they can sort it out for you. The main question is, do you want Google to sort it out for you or do you want to sort it out for Google?
Googler, Jonathan Simon, said:
Having separate Sitemaps with similar URLs for each site owner is not a problem. The Sitemaps system will properly handle any duplicate URLs found within the same Sitemap or across multiple Sitemaps.
Forum discussion at Google Groups.
