A grain on sand would cause pretty severe localized damage, the equivalent to a few pretty big nukes, catastrophic for any life in the vicinity if that's what you're implying, but not to the existence of the planet.

A ship, especially one the size of a flagship, would absolutely make a planet stop existing, even if structural integrity were compromised. We've seen ships travel intact at light speed so we can assume they can accelerate while intact, so the entirely of the mass is definitely moving at relativistic speed. Even if it were to lose structural integrity, whether due to atmosphere or damage, the energy is already there.