I guess it all depends on how you define 'damaging the liner' and 'big pain'.

The liner doesn't want to be wrinkled, the wrinkles will wear out sooner than a smooth liner and the pattern will probably fade earlier on the wrinkles than it would ordinarily because of vacuuming and general use (this is aesthetic, but the wrinkles aren't attractive either ) - you'll also have the ridges to catch debris. As the liner is only 3 years old, I'd opt to get them out now.

To get them out, basically you want to lower the water to ~ the level of the wrinkles, work them out and refill the pool while keeping them from reforming - what we do where I work is to basically reset the liner with vacs - you may or may not have to use the vacs, depending on the ease with which you can work the wrinkles out. (I know I've posted this stuff in the past ~ month - if you'd like I'll try to find it or, I'll just retypo ( ) it)

I think you are right about the ground water pushing the liner around - was the pool level low durring the wet period? if so, you may want to think about adding some drainage to the area or a well point or 2.