Since there have been millions of extinctions in the history of the earth, obviously yes, the overall ecosystem and sub-systems within it recover. They are not the same, of course; ecosystems evolve and change, just as individual species do.
Ecosystems are damaged by the loss of a species. An ecosystem may recover, but it can be substantially altered by the loss of a key species. This is called the domino effect, and it happens when a keystone species—one that has ecological connections to many others in the system—disappears. In the case of a predator being wiped out, the species that it feeds on may then overtake the system, which could choke other species out and cause any number of other harmful effects. In some cases it is possible that this could lead to the collapse of an ecosystem, as the disappearance of the blacktip shark off the coast of North Carolina did.
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