A) Because the Precursors didn't fight back. They simply observed the destruction the Forerunners were capable of. And their dominion stretches across the universe. Forerunners didn't come close to destroying them all. What did, however is... B) The way they tried to store themselves for extended periods of time. It was the Flood. Unfortunately, the Flood, well, did what Flood does, and pretty much deformed every one of them.

But if they were invincible surely the flood never would have killed them?

They used the Flood to store themselves for extended periods of time. They opened up to them (the Flood was created by them after all) and didn't foresee the results. Hell, the Flood didn't kill them, in actuality. Moreover just turned them into hollow shells of their former selves.