Forum Moderators: phranque
the most effective way of doing it would be to use 301 redirects from the old folders to the new - from www.mysite.com/en/ to www.mysite.com/
Avoid changing much else until the new set up has been thoroughly assimilated by the SEs, though adding new content should be fine.
I'd also get in the habit of using mysite.com/ rather than mysite.com/index.htm - and make sure all internal and incoming links do the same.