If you have a lot with the missing objects, use the eyedropper tool on them... it will show you if its overwritten by a custom object...
That doesn't necessarily mean that that specific item is overwriting it (at least it didn't work for me a couple of times. But in either case "with thumbnail there and object not showing" and "no thumbnail at all", it's custom content that's conflicting.
I take out my download folder, usually just the tables, if say, it's a table that's disappeared, and check to see if it has appeared, if it has, then I put half of everything (all tables) in, check, if it's still there, put the rest in 10 by 10, if the last 10 made it disappear again, I take those ten out and put them in one by one again. That way I can weed out the culprit. It takes some work, and I can't remember when an object went missing usually, and most of the time, the creator gets a few mails and has it fixed already. Good luck!