I was in the nether, crafted some golden apples and when I removed the recipe from the crafter and just so happened to visit the over world I saw the items I was just using on the floor by my terminal.

I believe this is also how I lost a shulker full of unbreaking 3 books.

My storage system is no where near full

If your inventory is full and the system can't place items in, it will drop, check the chunkloading around your base (Could be #255), make sure all of your chests are loaded.