I have a small stone under the liner on the floor of my pool. We had to have the liner replaced a few years ago, due to some flooding issues, and I think they probably just missed seeing it.
We called the guy who installed it, and he said to just take a mallet and a small towel, place the towel over the rock, and tap lightly on it with the mallet. He said the rock should recede easily this way.
I am a little nervous about the rock puncturing through the liner. Any thought?