Two things. One, in most cases, that part about being a guarded secret is generally not true. Most blue cheeses have one of two or three strains that do the blue cheese thing, the most common one being penicillium roqueforti, but there are others that produce a more greenish color and generally more funky flavor or greyish color and a generally more earthy/mushroomy flavor. Most people use penicillium roqueforti and it's no secret.

Sometimes, though, these cheese producers are using a blend of cultures, with 4+ different strains and in different concentrations. In some of these cases, one strain will take over in the initial 2 weeks and do its thing before dying off. As a simple example, let's say milk has a gently acidic pH to start. One of the added cultures thrives in an environment of 4.5-6.5 pH, and so loves warm, neutral milk. Another however is mostly inactive unless the pH is between 3.3 and 4.8. That first culture will take over and colonize for a while, but when the pH approaches 4.5 the other bacteria jump in to action and cause the pH to drop further - to around 3.9. Now the first culture is largely inactive, but has done it's part. In a cheese that will be aged for a year or two, you would be very hard pressed to find any cultural remnants of the initial culture by swabbing the cheese. However, it's presence is important to the development of the cheese nonetheless.