Hi all

I have a 18'x36' IG ~36,000 Gal with a 2 year-old vinyl liner. Last Spring when I opened I noticed some wrinkles/folds on the bottom on the shallow end. This past weekend when I opened there are more and larger wrinkles on the shallow end and the liner is obviously stretched on the walls. My thought is that I am possibly draining too low and taking pressure off of the sides allowing the liner to stretch (though I don't understand how this would result in the wrinkles.)
I've been lowering the water to just below the jets which happen to be about 3/4 to 1 foot below the bottom of the skimmer box. In all, this leaves only about 2' of water on the shallow end.
My question comes down to this: Is it OK to leave the jets underwater? Can I just plug them and siphon out the water from the lines and lower to just below the skimmer box?
Climate is St. Louis MO where winters can be anything from Arctic to tropical.