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Mapped domain indexed twice: as website and as subfolder

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Hi,

I have a multisite install with subfolders. Let’s say the main install is in http://www.mynetwork.com and subsites are:
1) http://www.mynetwork.com/subsite1 mapped to http://www.subsite1.com
2) http://www.mynetwork.com/subsite2 mapped to http://www.subsite2.com
etc.

I’ve checked that in google (site:www.mynetwork.com) both versions are indexed: that is http://www.mynetwork.com/subsite1 and http://www.subsite1.com

Time ago I used to add a line in robots.txt like the ones:
disallow /subsite1/

But now I’ve deleted all this “disallow” lines related to subsites, and the subsites started being indexed as subfolders.

Why? How is Google “finding” the unmapped versions? Some of them are mapped years ago, none of them are recent mapped websites.

How can I avoid it?

Thanks


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