For one thing, it's a shame you have to get rid of something you love so much, but I can understand that the lotus just take over, and you need to make the decision of what is more important - lilies or lotus.
Second, it could well be that some root got into the nooks and crannies of the liner, and survived that way.
But redoing a liner is a big deal. I just enlarged my pond this week, and THOUGHT we had the bottom all smooth and flat. Well, walking around in there the next day, I discovered a bump about the size of my fist, smack in the middle of the bottom, and the water pressure has pressed the liner tight around it, and I don't know what it is, but I worry if it's something sharp like a rock, it may wear a hole in the liner.
But it's way too much of a job to get it out - drain 1000 gallons, remove the flagstone, displace 100 lbs of liner to reach the object, then try to refit the liner back into place. Way too much work.
I say you just leave the pond as it is, and be diligent about hunting down any future lotus.