Well they may have them now, but the question should be did they have them in 2009 / 2010? If they had them, did they know they had them? Did they realise which song they belonged to. I'm sure the archivist(s) hadn't finished going through all of the material the estate had at that point.
We don't know who was storing the vocals, in what format, nor where they were stored. It's a guessing game but MJ's recording appeared to be sporadic and disorganised, particularly in those final years. We know, for example, that with the Will.i.am track MJ kept the vocals and Will kept the music. It's perfectly possible that if the Best Of Joy vocals were recorded separately to the rest of the song they could be stored on a different hard drive in a different location. The MJ Estate may not have managed to piece them together in time for the album version released on the Michael album.
as I said, it's all guesswork, but I agree with Mikky Dee there would have been a sound reason behind them being missing. They couldn't find them, they weren't good enough quality, the 'sound' didn't match the other vocals they had, there was a rights/payment dispute of some kind, or many other reasons. One day we may hear those lyrics, or maybe not.