Assume I have following query
MyModel.all().filter('transfered !=', True).fetch(limit = limit)
I am afraid it's not possible. The indexes only store references to your entity where there is a value for the given property.
I suggest you do a couple of things.
Reprocess the data to add some sort of sentinal value to all entities (possibly one of the valid values) that are missing the value. The sentinal value could be None, which is different to not having a value.
Set a default value on the property that is something such as None, so that you can query for items that have no explicit value, if that makes sense in your application. This guards against the possibility of future entities having no value set.