New Earth was a unique universe, as it was an amalgamation of Earth-One, Earth-Two, Earth-Four, Earth-S and Earth-X as a result of the multiverse partially collapsing during the Crisis, thereby creating a new reality.
The new history of the New Earth Universe was primarily the history of Earth-One, with additional aspects of Earth-Two, Earth-Four, Earth-S, and Earth-X folded in. As a result, although it superficially resembled the Pre-Crisis Earth-One, it was, in fact, a new Earth.
This was apparently not the case however, as other alternate universes were discovered to still exist, and even the ones that didn't, could be accessed through hypertime, because every timeline that ever existed was available to a person who used that method of time travel. This includes any timeline that existed prior to the Crisis.
The Super Friends' Earth, which was called Earth-1A, Earth-Thirty-Two among other names; was most likely still in existence, as Mr. Mxyzptlk and Bat-Mite traveled to that Earth, and unless they were travelling through hypertime, that's a good indication that Earth survived, even though the Crisis used bits of it to "create" New Earth.