I wanted to see how you guys do booze droppers for isolated dwarfs.... Last time I tried it demanded a shit tone of micro management....
A simple minecart route can fully automate the process. Dwarves load the cart full of booze and push it down the track, through two statues (blocking dwarf-access to the tracks), and dumping the booze in the isolated area. Dwarves in the isolated area drink the booze and load the empty containers back into the cart. Once the cart fills up it's pushed back out for a refill.
I noticed that (some of) my boulders were simply vanishing...
The game already has a "wear/damage" tracking system for objects, and Toady would very likely use it for "falling damage" much like it is now used for "fire damage", "combat damage", and "throwing damage". Having falling items simply disappear seems rather unlikely.
I tested dumping booze barrels down a 30+ z pit in v0.44.09. Whether dwarf-dumped, minecart-dumped, or "tossed" by a retracting bridge, all the barrels survived the plunge. I then set the dwarves to repeatedly load the barrels into the minecart and let it run a while. By the time all the booze had been consumed there still weren't any damaged or missing barrels.
I'm not sure where your missing items disappeared to, but if you post your save it might clarify the matter.