My understanding was the original audio was simply lost over time. Of course, all the missing color footage cut when they made The Menagerie version eventually turned up, so anything is possible.
A full audio recording (recording during a public broadcast of the 16mm version) exists, I’m trying to get my hands on it.
And no, not all color footage turned up, or at least was used for any of the restorations. Which was a big surprise to me, they didn’t even use all of the Menagerie footage for the restored versions