What happens when you play Abandon on a spell that was played for its Flow cost?

It will be banished when it attempts to leave the chain.

“[T]hen banish it” in Flow’s text is short for “if it would leave the chain after becoming a finalized chain item, and leaving the chain wasn’t instructed by its own execution, banish it instead.” Abandon returns the countered card to hand after countering it, but for the purposes of Flow’s “then banish it”, this is also leaving the chain. No matter how it happens, as long as the Flow spell leaving the chain wasn’t instructed by the execution of the spell itself, it will be banished.

This also applies to effects like Kai’Sa, Evolutionary from Origins, or Fizz, Trickster from Spiritforged.