You need to repay $27,000 *MINUS* the Social Security and Medicare taxes.
Your 2016 tax return has already credited you the Federal Income Tax withholding and State Income Tax Withholding. So you are 'keeping' that amount. Because you get to keep that benefit, you must repay that amount back to the employer.
You are presumably also 'keeping' your 401k contributions and insurance for that time period. Because you get to keep that benefit, you must repay that amount back to the employer.
To illustrate: Let's say the Federal and State income taxes were $3000, 401k and insurance of $1900, and Social Security/Medicare of $2100 ($7000 total).
You would repay your employer $24,900 ($27,000 minus $2100 of Social Security/Medicare). You would still keep the $3000 of credits on your 2016 tax return, and you would still keep the $1900 of 401k and insurance benefits. That will even everything out.
For simpler bookkeeping purposes, it is POSSIBLE your employer would ask you to pay $27,000, and at the same time, they would give you the reimbursement for Social Security/Medicare taxes ($2100 in the example).
For your 2017 tax return, you can report the repayment as Fanfare pointed out below.
