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It is deer. They like lilies. This article will help:
https://www.gardeningknowhow.com/plant-problems/pests/deer/deer-repellents.htm

It is definitely possible that the plant has been affected with blight, as this most commonly affects Asiatic lilies. I would remove and discard any affected plant material and repot with new soil. If the botrytis blight is severe, applying a fungicide can help prevent the disease from occurring on other plants in the garden.

It sounds like your plant may have thrips. They start by attacking the flowers. This article will help:
https://www.gardeningknowhow.com/plant-problems/pests/insects/controlling-thrips.htm

It is possible that the beetle is the source of the problem, but it is just as likely not the source. I would recommend treating the lilies with neem oil. Neem oil will kill both fungus and pest, which either could be your issue. Neem oil is safe for people and beneficial bugs though, so is ideal for treating for several issues at once.

These are bulbils, which can be planted. So, yes, you can remove them and grow more plants with them. Here is more information: https://www.gardeningknowhow.com/garden-how-to/propagation/propgen/what-are-bulbils.htm

Here is an article that will give you some ideas on what you should do. Based on the content of this article, a drop in temperature will help return the bulbs to their dormant state and it is recommended to put them in a very cold place like the back of a refrigerator. You could try it and see what happens. Good luck.

https://www.gardeningknowhow.com/ornamental/bulbs/bgen/how-to-store-bulbs-that-have-sprouted.htm