I have a similar pool and similar problem. Here's my story and a trick for you to try.
First my story: Last year after opening our 3 year vinyl IG with a poolcrete (sand and cement mixture) bottom I noticed that about 4 inches from where the side of the pool meets the hopper sides there was a line of what felt like rocks that had suddenly 'popped up'. I was worried that these could hurt the liner, and called the builder to come out and have a look.
He looked it over, and felt the bumps. He suggested that the high water table over the winter (it stays wet where I live) probably caused the liner to lift slightly because of the reduced water pressure caused by lowering the pool water level for winter. When the liner lifted it allowed tiny grains of poolcrete to fall from top edge that meets the steel walls.
His suggestion was not to worry.
The trick that make me feel better:
The builder suggested taking a piece of the liner and place it on the kitchen counter, then take a small grain of sand or very small piece of dirt and place between the liner and the counter. (I had a big piece left from where they cut the liner out around the steps). This tiny grain of sand no bigger than the head of a pin felt HUGE! I looked under my little 'test' to make sure it was just one grain of sand, and felt again. It felt like it was the size of a BB or even a little larger. The bumps in my pool were all about the same size or smaller.
I no longer worry about the bumps.
Your builder is right - draining and cutting your liner will expose you to a huge risk of leaks. The seams on most liners are 'heat welded' together. If they slice your liner they will use glue, and you are very prone to having future leaks. I wouldn't risk it.
By the way - I'm curious why you had to replace the liner in a 2 1/2 year old pool. I'm assuming some kind of accident or damage since most liners last 10-25 years.
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