I've seem to loose some bags when I drop them on the floor. As far as I know all my stuff moved over just fine, but in the process of rearranging my stuff, occasionally when I drop a bag from my inventory to the ground, it will have the sound effect of the bag dropping, but there is no bag.
Sometimes when you drop a bag, it will go on the floor where you are placing it, other times if you are too low for example, even though your mouse cursor may be in the middle of the house it will show the bag by the door. I understand both of these scenarios are desired behavior and have seen them for awhile. But there is a place between the two where the bag just seems to disappear and cannot be found. I have so far lost 3 bigger bags this way. It almost as it is going into an invisible basement.