I launch my MS from my desktop icon. The first time you login after this 'migration' you will get to see the EMS and GMS portal. You select one of them and it shutsdown because it will download or config a few things and then you just start it again and you get to the login page. This also happens if you reinstall MapleStory.
This EMS/GMS portal already existed since before Halloween patch I think. But now that the migration has completed the portal to EMS/GMS should show everytime from now on.