I find myself asking the same questions, but there are no definitive answers. In the case of Hieronymus his work was too monumental for later scribes to want to copy it down. They are fools for it, since I can name quite a few historians today who would be willing to kill for the chapter on Ipsos alone. Hieronymus history is the history of antiquity for a century. Had his work existed it would have been our most valuable historical source in the history of our species, hands down. Polybius wasn't an eye witness to the events he described, Thucydides' account is merely that of a conflict between two small states in the Aegean, and Herodotus' account is filled with inaccuracies. By contrast our Hieronymus was an eye witness to mostly everything he wrote about, contemporary to everything, thorough and scholarly in every aspect of his work, and his history encompassed so much territory to surpass everyone that had ever written history to the time of his death, and then afterwards until modernity and the rise of modern historical discourse. He not only wrote about Alexander, but about his successors, and continued to write about their successors, which included Pyrrhus' conflict with the Romans . I'm sure you already know all of this. I'm outlining everything because it is all the more sad that his work didn't survive for us to cherish it.

As for Ptolemy and other such historians the simple answer is that there was enough interest for later historians to use their accounts as the basis for their own works, but there was no interest to simply copy everything out of generosity for the future. If the works of Ptolemy, Hieronymus and Aristobulus were shorter then perhaps someone would have shown interest in copying, but alas they were either deemed too long or people simply wanted to show some originality. This is by no means necessarily bad, but it would have been better to have at least one primary source on the period. In that case we could contrast it with what the later historian wrote and make a judgement as to whether he reliably used his sources. The way things are we are just going to have to trust that Plutarch, Nepos, Polybius, Arrian, Curtius, and other authors put some effort in writing their abridged histories based on the histories of earlier authors.

As for the possibility of unearthing Hieronymus or Ptolemy, while I would not rule it out as a possibility altogether, it is nonetheless becoming less and less likely the more we allow those treasures to sit in dumps under horrible conditions which slowly but surely are destroying them. If we did find something then it wouldn't be much more than a few words on a ruined papyrus, but at least it would be something. There are many teams working hard to find manuscripts in the weirdest places. The Oxyrhynchus project found a history of the Greek world, or Hellenica, much like Xenophon's own version. Papyrology is s field worth investigating, so if you want to look up some discoveries, look up http://www.papyrology.ox.ac.uk/POxy/papyri/the_papyri.html for a start.