I don't know what type of travel system you have, but this is what we did with ours.

Our travel system let us clip the baby's car seat straight into the pushchair frame, so we used this as the pushchair we took to the gate. This was gate checked and arrived back on the carousel. Obviously the risk of it getting lost between the gate and the plane, and the plane and the carousel, is not zero, but it's also not significant.

The lie-flat crib element of the travel system was packed in a box and checked in as our extra piece of baby-related paraphernalia.