Depends on there the fungus is. It is not common that if your fungus is grown on those troublesome lens elements, they will reject your lens, because they have to tear up your lens to take out the affected lens element to clean. It's troublesome, and they may not necessary have the expertise or dust-free environment to do it.
I've been rejected once before. You may have luck with Fatigue bro if he is able to clean your lens for such scenarios.