If the lilies are kept wet, like moving them to a tub of water, they should survive the disturbance, blossoms intact. I have received water lilies from sellers that had blossom buds on them,a nd when I planted them and put them in water, the blossoms did open, so I wouldn't worry too much about that if you keep them from drying out and avoid shocking them too much.

You can thin out pretty much any plants at pretty much any time. Most are quite adaptable, and recover quickly. You might be able to get a lot of the debris off the bottom with a fine mesh pond or pool net.

I personally don't like anacharis. I just don't like the look of it. However, if you put koi in there, the koi will likely eat it as they get bigger, so they will keep it thinned for you. Koi love "salads", LOL.

If the bullfrogs are eating your young koi, either relocate the frogs or get bigger koi. I don't allow bullfrogs in my pond. They're native, so they can be relocated to lakes and wild ponds with no repercussion.