I am not a specialist on the subject, but I browsed a little for some literature on the subject and according to what I found vitamin K1 and K2 are both quite heat-stable, thus it seems unlikely that a relatively mild heat treatment like pasteurization could significantly affect their concentration in milk (or none was curious enough to study this subject).
Nevertheless, I would consider the time elapsed between milking and consumption, which is expected to be longer in the case of pasteurized milk, and thus oxidation of these vitamins could occur during storage of pasteurized milk. Also, in the case of bovine milk, pasteurized milk is most commonly homogenized, i.e. the milk fat globules are broken down to smaller droplets to avoid natural creaming. In this case the milk fat globule membrane loses its integrity and it might not protect the fat droplet from oxidation as it does in raw milk. In any case, you should consider the difference between the theoretical stability of a purified molecule and one immerged in a protecting surrounding environment...
I ignore if the heat treatment affects in any way the isomerization of these molecules.
Leonardo! Yes, oxidation and the membrane integrity issues would certainly make a lot of sense! Thank you! I am still just a baby in this research, so it helps to have more experienced brains helping out! ;-)! Vesna thank you for the compliment, and I hope your research is going well. I saw you sent me some things. I will look at them when I get a chance! Patrick, alas, I am not in a lab, nor am I qualified to find the answers organically. I am but a mere researcher. I rely on the smart ones like you guys!;-) Peter, yes, and I think Leonardo hit the nail on the head! Thanks all of you!