What was contributing to a notable decrease of slavery in the Upper South around the same time as the Deep South's cotton boom?
slavery certainly increased in the Deep South after the cotton gin made cotton profitable in that region. Yet this would not necessarily correspond to a decline of slavery on other parts of the South.
The major factor that led to the decrease in slavery in Upper South was the decline in agricultural productivity in that region. The slave economy in the Upper South had been dominated by tobacco in colonial times. By the end of the 18th century, the land was becoming exhausted. Tobacco in particular is very hard on soil, taking out nutrients and leaving the soil fairly infertile. As this happened, it became harder and harder to make good profits from large-scale staple crop agriculture in the Upper South. For this reason, there came to be less demand for slavery in that region and it was more profitable for slaveowners in the Upper South to sell their slaves in the areas where there was high demand and high prices.