The Meaning of Life, the Universe, and Everything.
I just finished a rather large build of a gold pigman farm above the bedrock ceiling, and left the game running for some time plugged into my spare monitor to keep an eye on it while I played a few other games.
So, before I leave myself idle, especially in a place like the nether, I stash my gear in a safe place, either a chest or in a shulker shell box stuffed into my ender chest storage. I am playing in an offline world, no person could have stolen the gear. Ghasts cannot spawn on the half slabs covering the farm, nor do they shoot random fireballs all over the place when they do. None the less, Im pretty sure I stashed my gear in a box on the lower level, just in case a ghast spawned and set it on fire shooting at me. I seem to think I removed all the chests once the spawning floor was built and moved them all to the lower floor just so a freak ghast appearance wouldn't wind up with them burned or exploded. The audio was on and I had the monitor next to me the whole time. Nothing attacked me, certainly nothing that could destroy a chest if I HAD in fact used a chest next to me on the idling platform. The four double chests that I would have logically used to stash them on the lower floor are in tact. All my gold collecting chests are in tact.
None the less, my elytra and diamond armor are nowhere to be found. Seems I stashed the tools in my ender chest, so I have them, but I cannot find the armor/elytra anywhere in any of the storage blocks on the farm. I cannot find them in my ender chests or the shulker boxes stored inside it. I cannot find them in ANY storage chest on my world. The ONLY thing I can conceive of, is if I did in fact use a chest nearby me on the idling platform, and a magma cube ignited it. Is that even a thing that can happen? Is there any known issue in the game that can cause items to just disappear from a chest?
I dont suppose theres a tool I can use to read my save file and locate the items that way?
Chests, like crafting tables, can be set on fire. However, they do not get destroyed by fire the way, say, a wooden log would. If fire is your only concern, and you are sure that you actually put the items in a chest, then your items are still safe in the chest. Chests are not blastproof, however, so a ghast fireball could potentially destroy them and the items in them would fall to the ground
It is possible that you clicked too fast and didn't actually put the items in the chest even though you thought you did. If the items were still being dragged by the cursor when you closed the chest, they would've ended up on the ground instead. If that is the case, they went unnoticed and despawned after 5 minutes of being left on the ground.
I don't know of any current bug that would just delete items from an inventory, unless there's some sort of sync/lag issue going on (these are usually resolved on their own after a restart, so you didn't actually lose the items even though you might think you did). I have this happen all the time in pure vanilla 1.13, since my computer is on the bottom boundary of running minecraft comfortably (I need Optifine to play smoothly, but I'm not going to mess around with beta Optifine versions since they've burned me in the past).
There are chunk-corruption scenarios that would reset a chunk back to a previous saved state, that would cause items in inventories to be overwritten. There should be more than 1 inventory affected, however, unless 1)that's all you have in the chunk or 2)you don't typically frequent those other inventories.
Best guess is you took the items off and stored them somehwere 'special'…
Are there any empty spaces in your ender chest? (This would be the most logical place to store the items unless it was alreadty full) If all the slots in your ender chest are occupied, then the items can not have been there and vanished.
Are there any empty spaces in "[t]he four double chests that [you] would have logically used to stash them on the lower floor"? (same logic)
Ditto the various shulkers…
Ender chests and shulkers are not flamable, nor are chests (although lava can produce fire in a block next to the a, the chest is unaffected).
Magma cubes do not start fires in any case.
A ghast fireball can destroy a chest, but (as you note) the chest would need to be either near you or directly between you and the gasht to be hit.
[There is a vanishingly small possiblity that a collision of two ghast fireballs might have diverted one into a randomly placed chest, but this can probably be ignored as a realistic possibility.]
There are issues with the game being glitchy but I've not heard of this causing chest contents to go missing other than during a world update [not an issue in the scenario you describe] or when items are being moved (as by a hopper line) across chunk boundaries [which seems unlikely in your case].
Were only one item to have gone missing, I might suggest that you inadvertently dropped it when you thought you placed it in a container [been there, done that >: ( ] and it then despawned, but this seems most unlikely with multiple items.
While I would put nothing beyond the possibilities when Ye Olde Glitche Monster comes out, my best guess is that you stored the gear someplace logical at the time, but not in retrospect... (One possibility, you took the armor off "someplace else" and traveled to the gold farm without replacing it [Been there, done that too]
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WARNING: I have an extemely "grindy" playstyle; YMMV — if this doesn't seem fun to you, mine what you can from it & bin the rest.
The Meaning of Life, the Universe, and Everything.
Thanks for each of your replies.
So far no luck finding the gear. I had considered I may have left it behind and then traveled to the farm, and as a result have repeatedly checked every chest I can conceive of in the farm, and anywhere in my world I can think of where I have a chest. Memory seems to indicate I flew up to the farm with my elytra and armor (Im rather certain it was with me on the farm in other words) rather than using the absurdly tall staircase, and temporarily stashed the gear in a storage box to keep it safely away from unforseen deaths.
To the best of my ability to remember, I had temporarily stashed the missing gear (if not the gear, some building materials) in one of the gold collection chests just before moving to the crafting station to compress it into blocks. I remember thinking "huh, was't my gear just hear? I must have put it somewhere nearby instead", and signed out of the game for the night. I logged back in, and seeing where I logged out thought "Oh yeah I need to grab my gear and the gold" and quickly set about trying to find it in the chests and shulkers stashed in the ender box.
I do remember the game cashing after I had been killed by a magma cube that escaped the spawning floor, although I had seen the gear afterwards after rebooting. I have also had a couple incidents of clicking on chests that would not bring up the inventory, but neither of those happened at the gold farm, and were in the overworld.
I also typically shift/click to instantly transfer gear and loot between storage, so it is unlikely (though not impossible I imagine) that I dropped it. I have also moved the drop-item key after I lost my beloved George Foreman 4000 flame sword to a creeper when I went to press the 2 key and fat fingered the Q after selecting it, just before the creeper exploded
Come to think, my axe Arbor Bane also vanished a week ago. Would be nice if I could trawl the data somehow for it's name and see what chunk it was in, if not my enchanted elytra and armor.