Don't worry about your water lilies. From my experience they are pretty indestructible and I have had tossed ones out of water and found them trying to grow in the compost pile. Just have faith and hopefully they didn't hurt the tuber (I have had raccoons eat the tubers).
I am also going to commit heresy and say any lilies that friends, or strangers can give you and you like the flower... take them. Hardy water lilies grow like iris and the tubers have to be divided/thinned occasionally. If you are worried about disease put them in a five gallon bucket full of water for a season. I have passed along my free lilies for literally decades.
Hope your plywood solution works. Raccoons are like little bears. If you ever have a little free time PBS had a great show called Raccoon Nation. I found it really interesting.
