If at any time the facts contradict the theory, the theory is discarded as false. A new one must be formed. The Holocaust deniers reverse this process. Therefore all documents are forgeries or mean something other than what they clearly seem to mean, and eyewitnesses to events which contradict their theory must be lying, mistaken, crazy, or victims of some form of coercion which caused themto give false testimony. There are other ways in which honest science can be distinguished from quackery.
Real scientists are cautious.
They look at possible alternative explanations. They look for possible sources of error. They explain any limitations or problems they know about. They shy away from making assumptions, and if they do have to make them, they explain and justify them openly. All conclusions are based on facts plus properly established theories, not speculation and unproven assumptions.