I have been holding the Golden Skull in the extra-planer chest to conserve room in my packs but I just noticed that all of the Skull gems I have acquired so far are now gone from it. I read about not putting crafted items in it or they loose their property's I assume that goes for the skull too? Is there no way to get them back or am I now screwed completely?
The problem here is that whatever you put into the chest actually gets stored only as a data string or something like that, and that is why every item that has additional properties outside its basic item data string like charges in a wand, crafted properties in weapons and armor and additional gems in a skull (at least this is how I've understood it works) gets reset to its basic state. Maybe you could console in the additional gems and add them to your skull again. Don't know the codes, though.