It means the recipe calls for a cup of flour total but that parts of it will be used in different places in the recipe.
The alternative would be to list the same ingredient in two different places on the ingredient list. Ingredient lists should be arranged in order of use according to the instructions.
Choco, sometimes you'll also see things like "halved" or "seperated in 2" (for example, "1 cup of sugar halved"), both of which tend to mean the same thing: the ingredient is divided into 2 (or more) portions to be used at different steps in the recipe.