Sorry but I don't have a save game to show as example (I was on the last push to destroy the Torians and win the game so I wasn't that concerned with not being able to use the planets I was taking for much) but whenever I invaded any tile that was not upgraded for use disappeared!
For example, I would send my transports into orbit and use Tidal Disruptors to gain the advantage. After I won the battle and then watched the screen to see what tile improvements were destroyed, the first ones to go were the Soil Enhancements, the Habitat Improvements, and the Terraforming tiles, THEN it would destroy other improvements but wouldn't include the terraforming improvements in the total number of tiles destroyed.. And the tiles they were upgrading were lost forever! Once I took control, I couldn't upgrade them myself!
I honestly don't know if it was the Tidal Disruptors or if any other invasion tecnique would also cause the same thing during an invasion...
Phu