It's common for high ground water to infiltrate under liners. This usually does not cause problems when (1) the liner is fully installed and (2) the pool water level is high. But what often happens is that people LOWER the pool water to winterize, and then suffer a 'floated liner' when ground water levels due to rains become higher then the level of water inside the pool.
In your case, the fact that you haven't suffered a 'floated liner' in the past indicates that, at your pool's location, ground water levels have never exceeded the water level INSIDE the liner.
But more urgently, I'm not sure how to advise you. I've installed a few liners, but not nearly enough to be an "experienced liner installer". You are sort of caught between a rock and a hard place. If it's raining, and you leave your liner-less the pool UNCOVERED, you are likely to suffer damage to the pool bottom . . . or even wall collapse. But if you install the liner OVER the water, you will not be able to 'seat it' properly.
What is sometimes done -- though I have no experience with it personally -- is that you bury 1 or more small sump pumps under the liner. But this is usually done on initial pool installation, when it's not such a pain to get a power line in, and a discharge pipe out, from behind the pool walls. I can think of a few possible ways to do it, with the pool deck already in place, but they are all 'kludges'.
Have you discussed this with your installer?
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