I recently flew into FLL and had a 12 hour layover before my morning FLL-EYW flight. I must have had some bad seafood that night because I was too sick to fly the next morning. I called CO and had them cancel my segment, but didn't re-schedule since I didn't know when I would feel better.

Later in the day when I felt better I decided to just rent a car and drive down to Key West. Now I'm wondering if I'll have any trouble with my return flight. I've read in the past about people's returns being canceled when they've skipped a middle segement of their itinery.

The CO website still shows my return flights confirmed and let me change my seats, so can I just assume it is okay or should I call CO again to confirm? (I don't want to call if it might bring to their attention something that they will want to charge me a fee for)

You better call again -- explain your situation - your downlegs will probably be cancelled - even if you can change them on co.com.

Should I expect to have to argue about a change fee? If so, does being ill have any merit in getting around it? (I just want to be prepared before I call)

IMHO - I would just explain rationally what happened -- that you did not want to "cheat" the system -- and they will make sure you are not charged a fee...