I had to do this very thing in the last liner I had. A year after the liner was installed, we noticed a couple of stones under it. We patched it with a piece of an old liner. It held just fine for another 5 years. Actually, those areas were still just fine, but we replaced the pool just a few weeks ago. The liner was actually still in good shape and those patches would have probably been fine for quite a few more years, but my pool walls were deteriorating.

It would be a big expense to drain the pool and refill. Filling a pool is costly. Especially since my sewer bill is based on my water bill so even though no water goes down the drain, when I filled the new pool recently, it impacted my water bill and sewer bill. I haven't gotten the two bills yet since the new pool was only installed about 3 weeks ago, but I'm guessing that between the two of them, I'll cost me about $500.

If I were you, I think I'd just keep patching as Ted suggested.