It seems, that in some cases, when a chest is being fed items through a hopper (maybe other pipes as well), it can "duplicate" the item, when you remove the original item the "duplicate" is removed and sorting the inventory after this seems to eat other items. I cannot duplicate this consistently, but obviously I have tried to work around it, as I dont want my items to disappear.

It seems to mostly work on unstackable items, as if I try to sort items in my mob farm while hoppers are feeding items in, quite often the weapons or armor is visually duplicated, once I remove the original from the chest, the duplicate is gone, and when I try to sort the chest again, the duplicate will overwrite one of the other items in the chest.

I also want to add to this bug of disappearing items. there is an issue when trying to sort the chest from the mod "nether chested" and the issue occurs when you have for example more than 64 items of a type, when sorting they dissapear.

so for example lets say we have 512 stone in one slot and lets say 511 on the other slot, so when we sort, the slot that had 511 will change to 64 deleting the exceeding items, because aparently the mod doesnt handle stacks of more than 64 that well so it tries to put like 64 and the rest is deleted.

se how on the first image we have a stack of 512 and another of 72, when sorting, the right one kept the 512 and the other turned to 64. also it does with multiple stacks so supposing I have all but one stacks of 512 and the last one < 511, all but one will change to 64 and the last one 512.