I had the same exact problem and I didn't do any syncing of any sorts. All my contacts just randomly disappeared from my address book, but remained in my favorites and recent call history. After I did all the advice on here and felt utterly hopeless, I went into setting on my phone. I tapped the iCloud, where I was prompted to merge my contacts. Since I didn't have any contacts listed in my address book anyway, I didn't have anything to loose. As soon as the merge was completed, all of my contacts were magically restored. This is what worked for me. Good luck!
i forgot to post about this but i did notice that if i re-added a contact, that would cause the old contact to reappear, complete with the thumbnail picture and everything. so the contacts were not gone, they were just hiding the new contact would be there as well, so i deleted the new one and i'm back. of course you have to know who was in your address book for this to work, so it's not a very good method of restoring anything.
i'm not surprised syncing with iCloud fixed it, as it probably either triggered this behavior or simply re-wrote all your contacts.