Why doesn't separating the layers change the equilibrium point?
Draining the aqueous phase cannot change anything. If the phases are in equillibrium before (both internally and with each other), they stay that way if they are separated.
Now if you add water to the aqueous phase, the reaction in the unpolar phase (which is saturated with water, as the phases are in equillibrium) is in the first moment not affected.
However the acid, alcohol and ester have different solubilities in the aqueous phase. That means the concentrations in the unpolar phase will change a bit, and so does the reaction equillibrium.
But: This is all irrelevant, because the reaction happens under reflux. While you are standing there with the cooled mixture in the separation funnel, the reaction rate is much lower, you will never notice a change.