What happens there is that submodules are checked out as a detached head. You'll see that when committing something in a submodule:

  Vienna-2:libgit2 pieter$ git commit -am "wawaa"
  [detached HEAD 8641889] wawaa

but you'll still have to know it :)

Of course, your changes aren't lost after the update. You can still get access to them from the reflog ('git reflog') or a simple "git checkout @{1}"