I'd leave $1,000 in the EF. You have to weigh your personal behavior patterns, and consider what the likelihood is of falling into the routine of using the credit card again.
We started paying down debt and wiped out our savings. Now we have $1,000 in the EF. Just the thought of swiping a credit card makes me sick to my stomach, so that was enough to setup the EF.
My math may be wrong here, but by keeping the $1,000 extra on your CC and having the EF will cost you about $8-$10 per month in interest. It depends on what your risk tolerance is!