Just because Letwin passed, doesn't mean a second referendum would.
Letwin was a chance to ensure that no-deal didn't happen, and they succeeded. Having a second referendum is completely different, and as i say, many Labour MP's in heavy leave voting areas will be dead against it out of fear of upsetting their constituents. Hell, even Labour MP's themselves don't think they have the numbers for that very reason.
You have to remember, a lot of Labour constituencies voted leave, and the MP's representing them want to respect their wishes. They could be whipped to vote for the amendment, but nothing is stopping them from abstaining, meaning that it'll be very difficult for it to pass. Plus, they've had numerous chances to have a second ref, even with May's deal, and if an extension is secured, Corbyn will want an election straight away.