This is very strange, as I often make custom buildings and place lights above the door and have not had this to happen.
I did have an instance where my door (I had used a tunnel door by mistake) was taken from the custom building and placed in a mine entrance. This was on a previous alpha so I do not know if that still happens.
@8BitCrab can probable elevate you member status, so you can post your stonehearth.log or save game file. It may provide additional clues as to what happen.
I remember something similar about a mine and a similar setup of lantern above a door and the hearthlings didn’t want to place the item. Doors disappearing is a relatively recent issue, often related to templates.
If this bug is reproducible with the steps you provided, @Kida, I’m sure @not_owen_wilson might want to take a look at it.