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Currently I have a structure as below:

I need to delete and re-create the site "thesite" but I don't want to lose the site "my".

Is this somehow possible?

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I see you've already accepted an answer, but just to clarify is /My a site within thesite site collection, or is /My a managed path to the My Site host site collection? – shufler Aug 15 '12 at 16:56
up vote -1 down vote accepted

If there are many such cases, then I would suggest you to use Metalogic Migration tools, if this is one of the case then , following should help.

Take a full backup of the subsite (http://thesite/my) (MySite)

stsadm -o backup -url "http://thesite/my (MySite)" -filename "<<add the file path>>"

Delete the sitecollection in central admin, take a backup of whole site collection before u delete , to be on safer side :)

recreate the root sitecollection (http://thesite) the way you want and restore the subsite back

stsadm -o restore -url "http://thesite/my (MySite)" -filename "<<add the file path>>" 

Hope it helps

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If we're assuming "/my (mysite)" is a site collection (using an explicit managed path of /my), there is no need to back it up as it is an independent site collection from the root site collection. Alternatively, if we assume /my is a site within the site collection, stsadm -o backup will not work; the export operation is needed – shufler Aug 15 '12 at 16:57

You could save the "my" site as a Site Template (including content) and then importing the resulting .stp/.wsp into the Site Template Gallery of the new "thesite". Then, create a site based on that template.

That would work if the "my" site is not heavy on data.

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Another option if you do not have much content in your site is to use:

Site Actions > Site Settings > Content and Structure (http://thesite/_layouts/sitemanager.aspx)

Right-click the site and select Move

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