I installed the Savage Empire from gog . When I started playing it I noticed there is a glitch that's not talked about anywhere online . With this glitch certain items and gear will disappear and will be lost permanently from the game . I had to learn this the hard way that whatever u set down on a crate in the lavatory that item will disappear permanently and be gone u won't be able to get that item back unless u restore to a previous save . Also if u tell one of yr party members to wait when u get back and ask them to join everything that character had before will be gone permanently that goes for every item and gear that character had on when telling them to wait . I've lost a valuable rifle at the lab when I set it on top of the crate and because I didn't catch it and already saved I can't get it back . tried looking online for answers could not find anything on it . So just be careful when playing this game u can lose valuable stuff .

From what I understand, the game (and Martian Dreams) uses Ultima 6's engine; therefore, item persistence should work the same way.

There are two types of objects (including items and actors): transient and permanent (for lack of better terms, unless someone knows of one). In general, items that exist at the start of the game are permanent, while items that are generated after the game starts (including those you buy, or that are found on random enemies) are transient. One notable exception is that quest items should always be permanent; in Ultima 6, reagents are also permanent for whatever reason (the spellbook menu counts only permanent instances of a reagent; if you use the Iolo cheat to cheat some reagents in (which will be transient), they won't be counted, but might still be consumed instead of permanent reagents). Items that are cheated via the Iolo cheat are always transient, even if quest items.

Now, here is how object garbage collection works when you leave the area:
* A transient object that is left out will disappear.
* A permanent object that is left out will remain where it is.
* A permanent container (like the chest in your room in Lord British's castle), will remain, and will protect its contents, so this is where you want to leave items you don't want to carry with you, but that you want to be able to get later.
* A transient container (like bags/chests dropped by enemies) will disappear, along with its transient contents. If there is a permanent item inside the container, it will be found on the floor.

So, in conclusion, you want to find a container (like a chest) that exists and is found on the ground when you enter an area for the first time, and store your extra stuff in there.

(In your case, try putting the item in the crate, rather than on top of it.)