If Rust Harvester leaves the battlefield before its last ability resolves, it won’t have a +1/+1 counter put on it when the ability resolves. Use its power as it last existed on the battlefield to determine how much damage is dealt.

If the target is illegal as Rust Harvester’s last ability tries to resolve, it won’t resolve and none of its effects will happen. You won’t put a +1/+1 counter on Rust Harvester.