I'm afraid that as far as I know the only control of Brown Rot is a continual application of chemical control.
It can cause devistation to all stone crops and although cleanliness is essential the spores of the disease are so persistent that some form of protection is needed so that they cannot develope.
Like with a lot of fungal problems, the chemicals available do not actually kill spores that have already germinated. They have to be there ready to prevent them from germinating in the first place.
So it's essential to get a protective coating on the plant ready to do so. That's why as the plant produces new timber , or the fruit grows, further applications are needed to protect this new ' naked ' material.