Yes it makes sense. It is suppose to negate the 3,000 you already got. Because you already got it. So it changes your credit from 6,000 to just the remaining 3,000 and removes the 3,000 you already got from your refund or increases the tax due.
At first the whole 6,000 is added to your refund (or reduced a tax due). Then you say you already got the Advance for half of it so it reduces the remaining amount back to 3,000 credit. You can't get the whole 6,000 credit now, only the remaining amount. If you adjust anything on your return of course it's going to change the bottom line tax due.
