My assumption has always been that Skarner's lore was just shifted to Shurima and adjusted to accomodate for the new local, so in my eyes:
- The Brackern are still a thing
- It was Shurima that caused the Brackern's downfall; Ascended might have also been involved
- The crystals dying is tied in to the desertification of their home
- The Brackern are underground either repopulating or hibernating or both
- They're waiting on Shurima to come back to life so to speak so the sand receeds and they can live above ground again
- The Arachia still exist, just in a different form (which seems to be the spires now)
- The Crystal Scar is still a place, it's just in Shurima now and refers to Skarner's domain and where the entrance to the Brackern's realm is located.
- Skarner's job has been moved in to the roll of active protector, so he probably misses his kind WAY MORE as he's been guarding them for god knows how long.
That's what I've assumed since his short lore was introduced, and with the introduction of the Crystal Spires, which basically function very similarly to the Arachia in his original Champion Judgement, I've only grown more confident in my assumption.
EDIT: As an additional note I'm waiting on the day they VU Crystal Scar to be in Shurima. I can practically see it.