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Not to sure why I did this. But I submitted the same sitemap for our .co.uk and .com domain.

Looking to put the .com domain on different hosting and create a new site for international customers using .com domain.

Should I remove all urls in google webmasters for the .com domain, guessing this won't have a negative effect on .co.uk stuff and add robot.txt to make sure the .com domain is not crawled?

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Is the content different on each domain? When you submit sitemaps in GWT doesn't it auto-fill the domain for you leaving just the path to the sitemap to fill in? If you happened to have two sitemap files in the same root folder and submitted the wrong one. I think the full URL's in the sitemap to the wrong domain is something Google will recognize and not crawl them. What did you do exactly? – Anagio Dec 19 '12 at 15:25

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Content for each domain is exactly the same. Pritty sure Google isn't penalising my site at the moment. Making sure it won't in the future.

There is only one sitemap file, all domain have the same route folders as under all with one hosting.

When setting up the site didn't have a clue so submitted exactly the same sitemap for .com and .co.uk. If you open up the sitemap linked to the .com it has .co.uk URL's.

Guessing it won't be a problem in the long run by the sound of things?

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You should move this answer to a comment you probably just hit the wrong input box. I'm a little confused on your setup. Each domain has the same content and same folder structure? All on one hosting that I get. But within that hosting account there should be two root folders one for each domain. So bottom line in Google Webmaster Tools. Delete any incorrect sitemaps associated with the wrong site. Re-submit the correct sitemap and that's about all you can do in GWT if there are any errors that will fix them over a few days to a week as far as Google recognizing the sitemap changes. – Anagio Dec 20 '12 at 19:18

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