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This may be a silly question, but can you pollinate a Copiapoa Hypogea from one of it's pups? I have a big clump of Hypogea and a few of the cactus have flowered and I was wondering if they could be pollinated.

As far as I know you'll need a completely different clone to produce seeds normally. Plants grown from pups are genetically identical and won't usually produce seeds when pollenated with what is essentially itself.
That being said there are some methods for self pollination you can try, though I cannot say if they will work. I did try a cement self-pollination method on my C. hypogea and got 5 seeds out of it. Though I have not tried sowing them yet.

thank you for your reply, I will look into that.

I have observed here that Copiapoa hypogea "lizard skin" is self fertile, so at least for lizard skin it is possible to self-pollinate it and have seeds.
Otherwise, for self-incompatible species, pollinating the pups of a given plant will not produce seeds (unless using these thechiques to overcome self incompatibility): the pups and the mother plant are genetically identical so they cant be used to pollinate one another