Last Jan., on flights MSY-phl-FCO, we took an earlier flight to phl, to avoid a tight connection. The GA in MSY apparently didn't scan in our tickets as we boarded, so we learned (at the very nice Envoy lounge) that our flight reservations and SEAT ASSIGNMENTS were cancelled.
We had had really nice seat assignments, over & back, which were lost. We did make our flights, but had totally new, and random, seat assignments over.
Although our reservation for the return, FCO-phl-MSY was restored, our seat assignments for that portion of the trip were not, but we weren't told that at the Envoy lounge - think I realized it when trying to check in on line, or just checking status of the flights/our reservation, on the return.
Fortunately loads were light, but it was irritating...
Don't miss a segment, at least not a 1st segment. It wipes out EVERYTHING on that reservation and unless there's a US mistake (as in our case) or some weather or mechanical issue, you're probably going to be out of luck. Hope this helps.
Happy travels