Hi! I just spoke to a couple of Veterinary Schools about this because I'm in the same boat. So far, a good majority of Vet schools create their own GPA. The one that the VMCAS use is a standard, but a really large portion of the schools don't necessarily follow it. They calculate your GPA using the VMCAS as a standard/starting point then use their own calculation system.
So far, all the Vet Schools I have talked to will still see the D in Chem, but they will not factor it into your calculated GPA come application time. They will only consider the Higher Grade. They made it clear, however, that that they only do this for science classes. So if you got a D in Calculus or English, and retake it and get an A, unfortunately (or fortunately depending on how you look at it), they will just average out the two and factor BOTH into your GPA because they aren't science classes. If you got a D in Chem, and an A in Chem when you retake it, they'll still see the D, but won't factor it into your GPA. They'll just use the A. They actually told me that it looks better when you retake it and do well because it means that you kind of learned from your mistake and you weren't willing to settle with said grade. One school (just an example out of the many schools I have spoken to) that really stressed this was UGA's Vet. They said if you have anything lower than a C in a science class, RETAKE IT because they do this. There is no limit as to how many classes you can retake I believe, and they'll only consider the higher grade received. Hope this helps and you find this comforting