Obviously, the Kents are a great example. Clark losing dad second after grown. Clark losing them younger, both living in present day

Jor-El - Ozymandias and I'm not even sure what current story is

Allura and Zor-El - died after sending Kara off, only later retconned to be in Phantom Zone. I can't remember if the were ever actually intended to be dead in post-COIE before we found them in Kandor. And more recently, Zor-El as Cyborg Superman.

Nora Allen - we all know that one

Silas Stone - originally he died shortly after Vic joined the Titans. Got to live in the universe reboot.

Trigon was actually intended to be dead and then brought back, right? I read it, but it was a while ago and I couldn't swear there wasn't a indication he was still alive.

Got any more to toss in?