This sounds like a problem I've been having in. When I invade a planet, any buildings that are on terraformed tiles simply disappear (and the ability to terraform those spots disappear along with them), but the buildings' effects sometimes remain afterwards until you reload the game. I haven't found much you can do about it other than taking the planet before it gets terraformed.

Edit: just noticed you said in DL. You should probably send in a bug report, since mine showed up in DA. Having more info to work with would probably make it easier for the devs to pinpoint and correct, especially since it happens in both versions of the game.