Did you by chance install RemoteTech Antennas for stock game mod after you deleted RT?
Because I was experiencing the same problem and just fixed it by renaming RemoteTech folder in gamedata (to RTAntennas). I wanted to remove RT but didn't want to start a new game so I downloaded RT Antennas to prevent vessel deletion because of missing parts.
EDIT: Nope doesn't work. It reappeared.