Disinfectant sprays are actually recommended for keeping whelping boxes safe. Between bedding changes you should disinfect the area, giving a good few sprays and wiping down the area. This kills any harmful bacteria and allows the new bedding to be laid on a clean surface. Just be sure that the spray has been firmly wiped away as leaving disinfectant residue can be a problem in itself. Your bitch could lick the wood or flooring, as could the puppies, which can lead to ingestion. Although this is probably not a worry for an adult dog, this could essentially poison new puppies. This is why you should spray, and then wipe down the area with clear water. Be sure to dry it afterward too so the area does not become damp and cold.