First of all, let's assume that we're not talking about a real-world situation (duh), so let's ignore physics. Obviously eventually we'd get to a scale where you'd have quantum effects.
So let's take it as a though exercise in math. One thing you don't quite specify is the timing of your operations, but the way you phrase it, I'll assume that you mean that each discrete step (filling the hole again by half) is done at a regular interval. In this case, the answer is: "You will never fill the hole in a finite amount of time."
What makes this a slightly different question from the usual Xeno's paradox is the introduction of discrete steps that are performed at a constant interval. Xeno phrases his paradox this way, too, but he calls up the image of motion at constant velocity... from which any calculus student would tell him that, as he shrinks the distances traveled, he also shrinks the times, so that series does converge within a finite timespan.