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Deer. While deer are not normally fond of echinacea, they will eat the young flowers, especially if they are hungry. Over population of the deer in many areas have left them starving, even in the height of summer and when they are like this, they will start to eat plants they would not normally eat.

The good news is that echinacea responds to deadheading (which is what the deer has done), and you should see another round of flowers this year.

Bringing it indoors should assure that it will return in spring. Echinacea are herbaceous perennials, meaning they die back in winter and return in spring. Just water once in awhile and move back outside when spring arrives.

It is up to you as far as cutting or leaving them. Either way is fine. Some people actually like to leave the plants and flower heads intact for the winter as the birds like to eat the seeds. It can provide some winter interest in the garden and then the plants can be cut back in the spring.

Yes, they do generally come back but you can still spread the seeds over the area you want them to grow in and cover slightly with soil (they don't need much). This can be done now or in early spring. The seeds will need water in the spring after winterizing (or following spring planting). In most cases, normal rainfall is enough but if you have a dry spring, you'll need to water the area.

Rabbits prefer tender new shoots and will eat coneflowers in spring. Stems and tough old leaves are woodchuck items. Your culprit could be a raccoon but I'm leaning toward woodchuck.

You can leave them there until you start to see a crowding problem. Try not to disturb them much when they are little. In the wild they establish themselves in dense patches, so they are adapted to these close quarters. When they spread too much, you can move some elsewhere, and thin the heard.