If everything is still canon...

[Bored at 3:00AM]

The retcon happened near the end of Doomsday Clock, Saturn Girl was erased (and replaced by the current one) because the reality in which Superboy joined the Legion was erased. Bendis's LOSH specifically references that the rebooted team wanted Jon, not Clark, and Clark was NOT a Legionnaire.

You said "Clark being Superboy is one thing that has not been returned to continuity". Both Doomsday Clock's ending and Bendis's LSH make it clear that Clark was Superboy, even if his time with the original LSH is still frustratingly unclear.

Clark as Superboy and him being a member of the LSH are two different things.

Clark's post-Crisis origin seems to be the canon one now.

What? The Byrne origin is not canon right now. It's still the broad strokes of Secret Origins and whatever else creators want to include. What makes you think that DC would inexplicably revert to an origin from 1986 that the character has long since moved past?

[bat39]

On a somewhat related note, one thing I've never understood five years on about Superman Reborn...does Clark remember the fact that he was 'split in two'? Does he have memories of both Superman Red (aka New 52 Superman) and Superman Blue (aka Pre-Flashpoint Superman)? Did they ever actually explain who 'split' Superman for that matter, and what Convergence had to do with it?

[Bored at 3:00AM]

On a somewhat related note, one thing I've never understood five years on about Superman Reborn...does Clark remember the fact that he was 'split in two'? Does he have memories of both Superman Red (aka New 52 Superman) and Superman Blue (aka Pre-Flashpoint Superman)? Did they ever actually explain who 'split' Superman for that matter, and what Convergence had to do with it?

A wizard did it.

[DABellWrites]

On a somewhat related note, one thing I've never understood five years on about Superman Reborn...does Clark remember the fact that he was 'split in two'? Does he have memories of both Superman Red (aka New 52 Superman) and Superman Blue (aka Pre-Flashpoint Superman)? Did they ever actually explain who 'split' Superman for that matter, and what Convergence had to do with it?

The answer is simple: they kicked New52 Supes out of continuity. But, DDC, Death Metal, and now Dark Crisis, have made it that somehow, the DC Universe has lost ten years and made it the New52. Which, didn't Superman five years prior to Geoff Johns Justice League? If you read Johns JL everyone had just got into costume.

[Clark_Kent]

How so? Doomsday Clock specifically showed Clark being Superboy in Smallville as a teenager and Bendis's LSH specifically referenced Clark as Superboy.

Yep, this right here. Clark being Superboy is precisely the reason the Kent's survived the crash. In Dr. Manhattan's altered reality, Clark wasn't Superboy because there were no examples to emulate. No stories for Pa Kent to tell his son to make him feel better, so Clark got the "keep yourself hidden" speech and the Kent's died. When Manhattan returned the lantern to Alan Scott's reach, Pa Kent then had hopeful stories about mystery men & heroes, and encouraged Clark to use his gifts. Thus, when the accident happens, Superboy is there to stop the truck & save the day.

I didn't read Bendis' LSH, but I did read his Superman and there's nothing there to suggest that Clark's time as Superboy had been altered from what Doomsday Clock showed us. I believe (I could be wrong) that Saturn Girl disappeared in Doomsday Clock because she was a Saturn Girl of the future that had been altered by Manhattan. Once things were 'fixed', she ceased to be & was replaced by the current one.