they should have replaced both fans at the same time...
i had a problem with the small fan not working, so the large fan came on to to compensate all the time and it sounded like a jet engine it was so loud
they replaced both fans at the same time, does not make sense to change just one when they are so closely connected to one another.
take it back to them and tell them they should have changed them both together! so its not your fault
it is a common problem with mk5gti I have seen a number of topics come up on forums about this over the past year.