Depends on the liner material. For materials that can be seamed it certainly is possible. Whether you want to or not is a personal choice. IMO liner needs to be seamed on a flat surface, like a concrete driveway. You might be able to lay a wood beam across a pond to do the seam.
However this isn't a job I would want to take on, not so much because of the seam, but because it could be a real pain getting the new hole in the right position. Normally we dig the hole and can position the liner to fit the hole. In your case the liner is in a fixed position.
Would just add the new pond and connect the two with a stream, unless space is a problem. If space is the issue I'd tear down the waterfall and rebuild. To me that's less work. With connected ponds you get almost all the benefits of a single pool pond...same water volume even if the fish can't swim in the total space.