YES, they will be going out of JFK tho, not ATL. wife and I were able to get 2 skysaver seats in business JFK to VCE next May, from there we will drive the Croatian coast to Dubrovnik and then fly home in business from Prague but we will have to go thru JFK to ATL to do it. I don't think they have plans of ATL to VCE anytime soon. We just came back from Edinburgh and we were also told the ATL to EDI would stop running and would start going out of JFK.
For some reason a lot of flights that were non-stops out of ATL are now going out of JFK!
I do remember someone mentioning they were waiting to change out the old seats and get new seats in the business section and that could be why some flights are no longer scheduled but I may be way out in right field on this theory.