I'm not so sure you need to get caught up in matching the noun+verb here. Try reading the sentence like this:
While digging in the Egyptian desert, paleontologists have found huge fossil bones from [what appears to be] the second most massive dinosaur that ever lived.
The above is answer choice D. Notice the section in brackets -- it can be crossed out and the sentence doesn't lose its meaning. In other words, [what appears to be] is a phrase.
While digging in the Egyptian desert, paleontologists have found huge fossil bones from [...] the second most massive dinosaur that ever lived.
Further, you can read this sentence as:
While digging in the Egyptian desert, paleontologists have found huge fossil bones from [X]
While digging in the Egyptian desert, paleontologists have found huge fossil bones from [what appears to be] [X]
On the versioning of that phrase [what appears to be], D would win over E. You don't want to say [what appear to be] since it's kind of describing [X] which we know is singular noun -- thus "appears" should be used not "appear".
Further, as a hint, simplicity wins on the GMAT when you're stuck between 2 choices -- most of the time. (D) is simpler, and avoids a comma and "which".
The latter parts of (D) are: "from what appears to be"
The latter parts of (E) are: ", which are from what appear to be"
Which one is simpler? (D) also wins.
The best way to set yourself up for success here is to do what we teach at GMAT Pill, breakdown sentences into phrases that can help simplify the sentence structure and give more insight into what groups of words go together. From there, you can make a better choice for what the best answer is.