Hi, I also had a problem similar to this. I have a Base on the Mun Surface, and I use a ship to transfer the fuel produced from the base on the Mun to the Space Station in orbit. I usually connect this ship to the Base on the surface with the pipes from KAS. The game and the mods were updated to the 1.2 version while the ship was landed and connected to the base through the KAS pipes. When I opened the game, the pipes visually weren't in place, but the entire Assembly (Base+Ship) were considered as one entity, as like the connection pipe was still in place. I tried to connect a new pipe and then detach it to see if I could undock the ship from the base, but it didn't work. Now I'll try to delete the connection ports both on the base and the ship and I'll edit the post with the result. If you have any other suggestions they would be very appreciated.
EDIT:
When I tried to detach the connection ports I discovered that all the inventories of the containers/seats on the base were empty. They weren't before the update (I had drills and other useful stuff in it). Now I'm sending the tools back up with another ship and I'll try again to detach the connection ports.