
I had this situation last year, and had had no chance to vaccinate the bitch before she was ready to be mated due to having been abroad when she came into season. I spoke to my vet, he looked up a lot of the vaccine manufacturer's data and said it should be fine to vaccinate her in season even though she had been mated. So she ended up being mated one day, vaccinated the next, mated the third day, and went on to have ten puppies all perfectly healthy.