Yes, with careful planning and execution, you can drain your pond without damaging the liner. Start by safely relocating any fish or plants in the pond to prevent harm. When draining, avoid sudden changes in water pressure, which can stress the liner, by draining the water gradually rather than all at once. A submersible pump or siphon can control the drainage rate, so you can monitor the progress closely.
Whatever the purpose for draining the pond, consider inspecting the liner while it is exposed for signs of wear or damage that may need addressing before refilling. If the pond has a lot of sediment or debris, go ahead and clear that out, using care to treat the liner gently.