I have found the answer:
After the last iTunes upgrade, and the subsequent syncing, iTunes syncs iTunes purchased items. All others it considers ‘pirated,’ and omits and deletes the files. I have a vast collection of songs that I laboriously digitized from my vinyl collection, and was hopping mad that iTunes nonchalantly deleted the files without any warning.
I was forced to buy a third party application to sync the songs back from my Touch to iTunes.
I learned that iTunes is built to sync TO iPhones/iPods/iPads, but not FROM them. Therefore syncing is a misleading verb. It should say that iTunes ‘overwrites.’ It’s supposed to ‘protect‘ copyright holders.