While it's undoubtedly tempting to leave an old liner in the hole to provide a secondary cushion (what harm could it cause?), this is one temptation you shouldn't indulge in. Even if your old liner had a few leaks in it, it's a non-porous material that can trap moisture and organic gases (like methane from decomposing muck) underneath your new liner. These trapped gasses create "whales"—massive bubbles under your new liner that can actually lift it off the floor of the pond. In a backyard pond, whales definitely aren't your friend.
So resist that temptation and remove the old liner. If you need that extra cushioning, use a dedicated geotextile underlayment. Underlayment fabrics are engineered to allow gasses to safely escape while providing a high-friction, puncture-resistant cushion for your new liner.
