Right now, no fix for this problem exists.
There have been some suggestions (thanks Scyve) on how to prevent it, but it's not that easy unfortunately, due to the mechanisms of creation of the different worldmap layers.
We'll try to look into it more indepth, but this may take a while. Meanwhile, if your house is afflicted, please just notify an admin.
The current workaround shall look like this:
The player sells the house in question, and an admin buys it, just so it's taken "out of order".
Then, all items will be carried from the last savegame backup which contained the undamaged house over to the live game, meaning an amin will drop the old items which poofed for the player to pick them up again and store them in any other house he bought.
At least, this bug should actually occur extremely rarely..