What happens when you cast a spell with multiple copies of Krark, the thumbless
On Gather, Krark has a ruling that covers this situation:

If you win the flip, but the spell that caused Krark’s triggered ability to trigger isn’t on the stack anymore (most likely because it was countered), the copy is still created.

This means that the flips still happen and the copies will still be created even if the spell has already been removed from the stack. In the ruling they suggest because of countering, but in this case it will work the same way for a earlier Krark returning the spell to hand.