I had the same problem a couple years ago. I did 2 drainings of about 1/2 the water.

If your pool is vinyl lined, be careful. If you have high ground water levels it could get interesting and other stretching could occur.

If you already did a 50% drain and had no problems, do it again. If you are seeing some new wrinkles then try this.

Get a huge plastic tarp or plastic sheet that will cover the pool and give you several feet extra in each dimension. put your fill hose on top of the plastic and start filling, and then start pumping out water from under the plastic in intervals to keep up with the fill. The level in the pool will not change.

When you are satisfied with the amount, pull the plastic sheet out. Done deal.

I would be shooting for a CYA level of about 40 or lower. It's easy to get it back up if you want to. As you have discovered its a pain to get it down.