Hi! You may be interested in my post here about textual criticism - the method we use to reconstruct ancient texts from the surviving manuscripts.

As for your second question, there are tons of stuff we know existed that have been entirely or nearly entirely lost. Almost the complete genre of Roman historical drama is lost. We have one complete work and a few quotes. Besides Caesar, the whole genre of commentarii - first hand accounts of generals - is lost. We know Cicero and Sulla, among others, wrote such accounts, but Caesar's is the only one left. We know about tons of histories that are lost. Pollio, one of Caesar's officers, wrote a history from his first hand experience of Caesar's civil war, and we only know it by reputation. Lots of philosophy is lost. We know Aristotle wrote Platonic-style dialogues, but none survive. One could write a nearly endless list of such lost works.

How important any of these are for historians depends on the use you want to make of them. Aristotle's lost dialogues don't do much for me personally - I'd love to have Sulla's commentarii - but for a historian of ideas or something they would be invaluable.