Regarding disappearing items, GoMule allows you to equip a two-handed weapon (or perhaps just certain kinds of them) and a shield and when starting a game with that character, the shield will disappear. I had this once and luckily it was just Moser's or so. I also remember an incident when opening the "all" entry while having stashes and/or characters open, so I'm closing stashes and characters before opening the "all" entry and vice versa.
Regarding differing stashes and inventories, I'm missing support for classic. It's pretty frustrating if character A finds a great item for character B without being able to mule it. Once I destroyed a classic sorceress by muling stuff to or from her with GoMule. Neither the game nor GoMule could open the .d2s file anymore. I took care that I was just putting stuff into the proper top left part of the stash and that no expansion stuff was involved, but it happened anyway.