I don't think it so much deer damage but I do rodent. I do not think squirrel. They get blamed for so much damage they don't do. Deer won't go to the base of a lily to munch.......and the lily would not still be standing and I see no way they could get their heads down to ground level inside that tiny cage. Something is either climbing up the cage and into the lilies or has a hole in the soil under those leaves. Vole, mouse, rat, chipmunk.

They could be white flies if they fly at all or white aphids. Both will suck the life out of your plants. First I'd take them outside in a shady spot and wash them off with a good spray of the hose. Be sure to get the undersides of the leaves. That will get quite a few of them. When they dry off spray them with neem oil--it's a green product. Again get the undersides of the leaves. You may have to repeat or just use the Neem to make sure they are all gone. All these small bugs have very short breeding and hatching cycles, so if you don't get them all they can reinfect Even if they are something other than I said--like spder mites, this treatment will work

Roots can stand a lot of jostling. Get a trowel in the pot and loosen the root ball around the edges. If it's not too root bound, you should be able to tease it out. Not critical yet. Hack that towering stem off when you can. It's not critical to do it right now, but it will make re-potting a lot easier. I would treat the spider mites first. You can pull off the webs with a paper towel then apply insecticidal soap. Read the directions and soak the little buggers. Your watering scheme is working - the plant has gotten this far - so keep at it for now. Try to get it more light. Closer to window and lower so all the leaves get some light. Peppers are tough. It will pull through. Dennis

This is from a link above. It reads well. If nothing else it is worth a notation, in my mind at least. Peppers Are Wilting: What To Do For Wilted Pepper Plants - If your peppers are wilting suddenly, developing large yellow areas and drooping (especially if this starts on the bottom leaves and moves upward) despite adequate watering, fungal wilt is probably to blame. Spotted wilt virus is a less common cause of wilted pepper plants, but if your plant’s leaves are dotted with brown or black spots or unusual yellow lines or circles and the symptoms move through the plant from the top down, it is very likely the cause. Occasionally, bacterial pepper wilt may affect your plants. Pepper plants will wilt and die quickly and upon inspection, the inner stems may be dark, watery and hollow.