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This is called alternate bearing. The reason for it is that while a pecan is using carbohydrates to fill the kernels in one fall season, it's not doing a good job of setting buds for next year. The tree is dedicating all its fuel to this year's fruit.
Then, the next year with a very light crop, the tree has plenty of extra carbohydrates to set buds for the following year. This alternate bearing cycle was first noticed by Spanish explorer Cabeza De Vaca back in the 1500s.