If they had done half the herd then they would have kept the unvaccinated half separate or marked the vaccinated ones somehow.
In many places it's common to have ear tags with a unique (to the herd) number or some other identifier on a cow.
Stock have a lot of things happen to them each year, and while paint is a very simple way to mark for some things, it's also generally a very good idea to have stuff written down.
(In the case of vaccines, you bet I'd use paint unless there's some compelling reason not to).
Just remembered that also there's a lot of automation on the farm these days based on RFID implants in the animals. They walk past a reader, the system records whatever was done. I believe in some cases animals that come back in for another round can automatically be 'rejected' as well.