Same problem here

i had to add one on my Makuta Class Cruiser's System Core

That was a limitation of the original code, fixed in today's recode. I haven't made it recursive (so you can't have pistons on pistons on pistons all disappearing) because that would add unnecessary load to the engine and maybe lag, but grids attached to the main grid via one rotor or piston will definitely disappear. Ships attached via connectors will also still need their own cloak block.