[PvK]

That is really strange. Never heard of facilities just vanishing - did you study the combat replay during which the homeworld went from 4 to 2 cultural centers? Did the planet get hit? If so, with what? My only thoughts were already mentioned:

* that maybe there was damage to the planet during the combat

I thought about the AI minister scrap idea too, if you have that on, but I don't think so - unless you have the minister on AND changed the colony type of your homeworld to something other than Homeworld.

PvK