I am sure some of the experienced breeders can help you. As Dvlshangel985 said, it is possible to spay during pregnancy.
Also, just a note on the brother/sister mating: I know it sounds really icky, but it's actually very common for breeders to mate related dogs to build consistency in their lines. So yes, it's unfortunate that an unplanned mating occurred, but "incest" is not the same for dogs as it is for people. Hope that makes you feel a little better.
Also, this is coming from someone who has never bred a dog, but Thor has vomited yellow bile before, and he definitely wasn't pregnant.
This can also happen if their stomachs get too empty. Keeping my fingers crossed she isn't preggers.