I am not sure because I have always checked luggage at my origin flight before arriving in Istanbul.
I will say, however, that I did have some issues trying to check my luggage early with Turkish Airlines in Tel Aviv a few months ago. My traveling companions were on an earlier flight with another airline. I figured that we would all go to the airport together, and I would check my luggage and then hang out for a few hours. Turkish told me that I was too early, and that they wouldn't let me check my luggage. I was stuck hanging out with my luggage for about two hours. Ugh.
If worse comes to worse, there is a luggage check just outside the airside Yotel. I checked a small bag for several hours after I checked out of the Yotel, and I don't recall it being expensive.