toward the end, when the... (spoiler alert)

Agreed

Er...Echo used his supe advanced Space magic to fill the ground after he left?...Maybe?

Well not necessarily! The ship might've caved the hole out. Means it could e created a sturdy hollow cave that would've lasted for a few more days, till everyone moved away. And then it could collapse without any human harm!

Or the ship could've replaced the hollow with something else through its energy transfer!