Yes, the split happens when it goes to airport control and happens on CO and UA and is unavoidable. I always have to keep an eye on it and take us off the upgrade list if I don't want us to get split up. It happened a lot when we were different levels. When I do clear and she doesn't she lets me have the seat since I have to work the next day, she gets to sleep (What a wife, huh?!)

Actually more recently we prefer to sit together even though we give up an F seat. We also book window and aisle and I slide to middle if the middle gets taken and give the aisle to the person in the middle seat. Makes for someone very happy on a transcon! ... well most of the time. One woman was so thankful offering to buy us drinks etc. etc. which we declined, but the other day the guy didn't say a word, not even a thanks! To each their own...

So, it sounds better to keep them split then. Also helps with my company booking policy... I am supposed to use our travel agency (ugh) for my ticket at least.