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In Google Webmaster Tools, if I target the main folder (e.g. example.com) to the UK, and a subfolder (e.g. example.com/en-us) to the US, will these settings conflict?

I know how to add a subdirectory as a separate site in GWT, but I'm concerned that setting a country target for the main folder will override the country target for the subfolder, and our efforts to launch our site in another country using a subfolder will be wasted!

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It shouldn't. You need to add each "domain sub folder" as a "new site" in your WMT panel, then individually GEO target them to your specific area. Also, if your main domain "www.example.com" is verified with your WMT, you'll get your other "domain sub folder" automatically

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I have targeted multiple subfolders before to different countries than the main root and it hasn't had a detrimental effect on the main site.

Also Google give this as an example, which I don't think they would if it could have an adverse effect

Multi-regional and multilingual sites

Subdirectories with gTLDs

example.com/de/

Can use Webmaster Tools geotargeting

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