Removing the root part of a ship in the VAB while the CLS window is open breaks the mod: the window stops updating, and it can no longer be opened and closed from the toolbar. The problem can be fixed by exiting and re-entering the VAB.

Deleting the ship while the window is closed causes no ill effects. Deleting any part other than the root causes no ill effects.

Thanks for this issue report. It was caused by that situation simply not being handled and so an exception being thrown. A fix as been committed, and it will be in the next release.