I had the same issue (Southwest canceled our original flight) - except ours is now getting in 2 and 1/2 hours later. When I checked in for the rental online, I was able to change the flight number. I'm hoping that is enough and that they don't give our rental away. I did try calling, however I'm not very confident in the response I got from the call center ("Oh it'll be no problem!") Our rental came up like $500 more if I changed the times, so that's not happening - I'm just hoping for the best!