You will get rebooked. Since you don't have status yet, you won't get top priority. It always helps to have a plan so you should research what will work for you if you do have a misconnect. Presenting the GA with something that works greatly increases your chances of success. Don't worry about fare differences on the rescheduled flights, that doesn't come into play.

If for example, you're late and misconnect on the ATL-CVG and there are no other flights that will get you to yur final destination in a reasonable time frame, you can let the GA know that you can be rerouted to ATL-JFK, skipping CVG and then request ORC after the trip. Important to let the GA know that youu would accept it but are not specifically requesting it, otherwise ORC might be denied due to a voluntary reroute.

Things to keep in mind for any future MR's. Avoid places like JFK in winter due to potential weather delays. Avoid connection points that don't have a lot of fall back and reroute capabilities so you don't get stuck somewhere with no place to go. Example: I have a LGA-ATL-SFO-ATL-LGA 4 hour turn in March. If ATL gets 1/10" of snow and shuts down I can get rerouted back via MSP or DTW and even accept a co-terminal to JFK which opens up direct/SLC/SEA/CVG. Lots of ways to get back.

As always, if you have a plan - you probably won't need it. If you don't, you may have lots of time to think about why you didn't have one.