Is this abandonment representative of evolution theory in general? Has it been challenged over time and accepted by the scientific community?
The Tree of Life was officially revised in 2000. The current tree shows chronological overlaps that are impossible if life had one single common ancestor. This has not sunk in universally as yet, but most working micro-biological palentologists now accept it. Since it is based on DNA mutation distance calculations for ribosomes, it will be very hard to mount a challenge at this point. We don't revise the root of the Tree of Life on a whim.