You won't be able to reuse the liner. Many have tried - don't think anyone has been successful. The liners are made small and then stretch when filled with water. When the water is drained they shrink. But then the vinyl has lost its elasticity (from the UV, chlorine, etc) and it won't stretch back to full size when you fill it with water again.
Also, like I think you are trying to state - you will never get the holes for the cutout to align again - that is why you cut them out after you fill the pool. If you have built the walls and don't have a new liner but just looking to fill the old liner to keep it stable during winter you MIGHT be able to make this work but not filling it beyond the cutouts. But you would have to drain all the water again in the spring and put in a new liner. You should be able to get a deal on a new liner from you local pool dealer at this time of the year.