If you ever end up with empty related records, the culprit might be these auto-generated objects that get created with you call certain magic methods on an object.

if ($user->Email->exists()) {
    // User has e-mail
} else {
    // User does not have a e-mail
}

$user->clearRelated('Email');

“Because Doctrine will automatically create a new Email object if the user does not have one, we need to clear that reference so that if we were to call $user->save() it wouldn’t save a blank Email record for the User.” – http://www.doctrine-project.org/documentation/manual/1_2/en/working-with-models

A better method might be:

if ($user->relatedExists('Email')) {
// now we won't get an empty Email record when we save $user
}