Can this redundancy affect the molecular structure and will affect the nutrient content of the milk itself?
Answers:
Why would you need to pasteurize it twice?
I'm not axiom you couldn't, you could if you wanted to... But coconut milk and cow's milk are not equal.
Anyway, if you heat up coconut milk (i.e. boil it for a long time) the hose will evaporate, leaving coconut grease and caramelized solids on the side and bottom of your pot (or whatever you used to warmness the coconut milk). So if you're not after coconut oil, freshly boil it for a couple of minutes to kill any germs. Good luck.
Other Answers:
no way u can not do this!! engender you very off-colour
buy another one so you will have afresh coconut milk.