In that case, enter the EIN from the 1099. When the IRS sees a 1099 and W-2 from the same employer in the same year, it is clear that there may be an error.
Now that the EINs do not match, you may be questioned from the IRS if the 1099 really should have been wages. It should have been. You will be able to easily explain the situation, with a letter in response if they reach out to you.
