We want to move our .co.uk website to a .com one. Will that affect rankings on the UK?
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Hi
The preferred and best geo-targeting strategy is to have individual sites targeting individual countries but as you mention this is usually reserved for big brands with big budgets since is the most expensive option.
However you already have both so i would be tempted to keep that going if i were you
You can avoid dupe content issues by correctly deploying hreflang attributes as well as geo-targeting both sites to their preferred regions in Google Webmaster tools (you should also do this for .com and .com/uk if you go that route too)
In addition you should have country specific content and other signals like local addresses and country specific social media sites pointing to each
All Best
Dan -
heres some other resources and threads since ive been looking into this in depth recently:
This International SEO checklist is great: http://moz.com/blog/the-international-seo-checklist
And a Q&A thread i started with some questions i still had after looking at the checklist
http://moz.com/community/q/international-seo-subfolders-user-journey-etc
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Thank you!
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My pleasure and good luck
International SEO is a bit of a minefield with no absolutely correct way of doing things, so enjoy the challenge & best of luck

All Best
Dan