We have a multi regional website which uses a two character string after the main domain to define which region's content to show e.g.
http://www.example.com/uk/ is the domain with English content specifically targeted at the UK.
There are a few pages which exist on all of the versions of the website (home page, about page, contact page). However much of the content is region specific and the structure differs somewhat depending on which region you are viewing from.
What would be the best way to implement hreflang tags based on the fact that the sites aren't set up as multi-language with the same content but are slightly different websites for each targeted region?
Also, for some reason each regional version of the website has been set up as a separate site in Webmaster Tools. We're thinking about deleting the existing entries for the website from Webmaster Tools and setting up a new single entry that covers the whole website instead of having one for each region. Could this be detrimental in any way?