They could very well be too big to birth. I would check with your vet and see what can be done if anything if she would have trouble birthing. You won't know for quite a while if she is actually bred. At two weeks you can palpitate if you are experienced in doing so. If not then you won't know until she shows signs of nesting or you can feel the babies moving in her belly closer to when they would be due.
I am curious as to why you say this. Is your theory that she won't produce as many eggs if she breeds with a Flemish Giant? If the babies are the same size wouldn't she have the same number? I don't know, I am just asking, I have raised a great number of rabbits in the past but I have not had Mini Lops mostly the larger breeds. I am very curious about this.