I also recieved that message
I got the same message this AM as DL changed the flight time of my JFK to SAN flight in September. Originally I had 35 minutes to make my connection in SAN and as since this was a MR I was a bit concerned. With the new flight time I now have nearly 2.5 hours in SAN to make my connection but I still recieved the message "you may miss your connection" I thoroughly checked the flight times/days etc to confirm there wasn't an issue. I just figured the algorithm they are using to predict a potential missed connect had a goof. I'm flying JFK to SAN to ATL to ICT and then back to LGA through SAN/ATL. it's a 36 hour, 6 leg MR. i'm going to be a tired puppy. LOL
For you I wouldn't worry about it. If the flight your own out of JFK is the last flight of the day to FRA you might consider SDC'ing from ATL to JFK so you can give yourself a bigger cushion. Otherwise you might have to spend a night in NYC if you miss the last flight out.