IRS will deposit your refund, less the amount withheld according to the bottom-up rule- see What if a mistake on my return decreases the amount of my refund?

You will receive a letter from IRS explaining why a portion of your refund was withheld, the effect on your direct deposit(s), and what information you need to provide to verify your EITC eligibility. If IRS later determines you are eligible to receive the credit, the agency will deposit the amount withheld into the first account you designated on Form 8888.

Source: www.irs.gov