If the issue started after Harvey, try applying a systemic fungicide now (even though we're heading into winter), again in early March and again in late May. Use Monterrey Agri-fos and follow the directions on the label.
My mother has a bunch of pecan trees, she was getting a bunch of bad pecans earlier in the pecan season. Most, if not all were bad. But the pecans that are dropping later many of those are good. She said it was because of the lack of rain, when the pecans were blooming and first started growing. Later we got lots of rain. Whatever the problem is, it seems to have affected our hickory trees also, I have not found any hickory nuts this year.
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